data_5908 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID 5908 _Entry.Title ; Backbone 1HN and 15N Chemical Shift Assignments for Sac7d V30I ; _Entry.Type macromolecule _Entry.Version_type original _Entry.Submission_date 2003-08-19 _Entry.Accession_date 2003-08-19 _Entry.Last_release_date 2003-10-06 _Entry.Original_release_date 2003-10-06 _Entry.Origination author _Entry.NMR_STAR_version 3.1.1.61 _Entry.Original_NMR_STAR_version 2.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype . _Entry.Details . _Entry.BMRB_internal_directory_name . loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.First_initial _Entry_author.Middle_initials _Entry_author.Family_title _Entry_author.Entry_ID 1 Andrew Clark . T. . 5908 2 Bradford McCrary . S. . 5908 3 Stephen Edmondson . P. . 5908 4 John Shriver . W. . 5908 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 5908 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '1H chemical shifts' 67 5908 '15N chemical shifts' 66 5908 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 . . 2003-10-06 2003-08-19 original author . 5908 stop_ loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID BMRB 5905 'Sac7d monomer' 5908 BMRB 5909 'Sso7d monomer' 5908 BMRB 5910 'Sso7d monomer mutant' 5908 stop_ save_ ############### # Citations # ############### save_entry_citation _Citation.Sf_category citations _Citation.Sf_framecode entry_citation _Citation.Entry_ID 5908 _Citation.ID 1 _Citation.Class 'entry citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID . _Citation.Full_citation . _Citation.Title ; Thermodynamics of Hydrophobic Core Packing in the Thermophile Proteins Sac7d and Sso7d ; _Citation.Status 'in preparation' _Citation.Type journal _Citation.Journal_abbrev 'J. Mol. Biol.' _Citation.Journal_name_full . _Citation.Journal_volume . _Citation.Journal_issue . _Citation.Journal_ASTM . _Citation.Journal_ISSN . _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first . _Citation.Page_last . _Citation.Year . _Citation.Details . loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 Andrew Clark . T. . 5908 1 2 Bradford McCrary . S. . 5908 1 3 Stephen Edmondson . P. . 5908 1 4 John Shriver . W. . 5908 1 stop_ loop_ _Citation_keyword.Keyword _Citation_keyword.Entry_ID _Citation_keyword.Citation_ID hyperthermophile 5908 1 Sulfolobus 5908 1 calorimetry 5908 1 'nuclear magnetic resonance' 5908 1 stop_ save_ save_references_1 _Citation.Sf_category citations _Citation.Sf_framecode references_1 _Citation.Entry_ID 5908 _Citation.ID 2 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 12666159 _Citation.Full_citation ; Bosch D, Campillo M, Pardo L. J Comput Chem. 2003 Apr 30;24(6):682-91 ; _Citation.Title 'Binding of proteins to the minor groove of DNA: what are the structural and energetic determinants for kinking a basepair step?' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev . _Citation.Journal_name_full 'Journal of computational chemistry' _Citation.Journal_volume 24 _Citation.Journal_issue 6 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0192-8651 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 682 _Citation.Page_last 691 _Citation.Year 2003 _Citation.Details ; The structural and energetic determinants for kinking a basepair step by minor groove-insertion of the protein side chains of PurR, LacI, LEF-1, IHF, Sac7d, and Sso7d, have been calculated by molecular dynamics/potential of mean force simulations. The structural determinants of the kinked structures are: two contiguous furanose rings achieve different conformations, in the region of C3'endo (A-DNA) and C2'endo (B-DNA); the chi torsion angle always takes values characteristic of the C2'endo conformation of B-DNA, independently of sugar puckering; and protein side chain insertion increases slide (from negative to positive values), rise, and roll, and decreases twist. The energetic determinants of DNA kinking are: the conformational transition of the sugar-phosphate backbone is not energetically demanding; the relative importance of the interbase parameters in the free energy penalty is slide, followed by twist and rise, and concluding with shift and roll; and the characteristic increase of roll and decrease of twist, upon side chain insertion, tends to stabilize the process of DNA kinking. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 David Bosch D. . . 5908 2 2 Mercedes Campillo M. . . 5908 2 3 Leonardo Pardo L. . . 5908 2 stop_ save_ save_references_2 _Citation.Sf_category citations _Citation.Sf_framecode references_2 _Citation.Entry_ID 5908 _Citation.ID 3 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 12060682 _Citation.Full_citation ; Napoli A, Zivanovic Y, Bocs C, Buhler C, Rossi M, Forterre P, Ciaramella M. Nucleic Acids Res. 2002 Jun 15;30(12):2656-62. ; _Citation.Title 'DNA bending, compaction and negative supercoiling by the architectural protein Sso7d of Sulfolobus solfataricus.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Nucleic Acids Res.' _Citation.Journal_name_full 'Nucleic acids research' _Citation.Journal_volume 30 _Citation.Journal_issue 12 _Citation.Journal_ASTM . _Citation.Journal_ISSN 1362-4962 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 2656 _Citation.Page_last 2662 _Citation.Year 2002 _Citation.Details ; Members of the Sso7d/Sac7d family are small, abundant, non-specific DNA-binding proteins of the hyperthermophilic Archaea SULFOLOBUS: Crystal structures of these proteins in complex with oligonucleotides showed that they induce changes in the helical twist and marked DNA bending. On this basis they have been suggested to play a role in organising chromatin structures in these prokaryotes, which lack histones. We report functional in vitro assays to investigate the effects of the observed Sso7d-induced structural modifications on DNA geometry and topology. We show that binding of multiple Sso7d molecules to short DNA fragments induces significant curvature and reduces the stiffness of the complex. Sso7d induces negative supercoiling of DNA molecules of any topology (relaxed, positively or negatively supercoiled) and in physiological conditions of temperature and template topology. Binding of Sso7d induces compaction of positively supercoiled and relaxed DNA molecules, but not of negatively supercoiled ones. Finally, Sso7d inhibits the positive supercoiling activity of the thermophile-specific enzyme reverse gyrase. The proposed biological relevance of these observations is that these proteins might model the behaviour of DNA in constrained chromatin environments. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 Alessandra Napoli A. . . 5908 3 2 Yvan Zivanovic Y. . . 5908 3 3 Chantal Bocs C. . . 5908 3 4 Cyril Buhler C. . . 5908 3 5 Mose' Rossi M. . . 5908 3 6 Patrick Forterre P. . . 5908 3 7 Maria Ciaramella M. . . 5908 3 stop_ save_ save_references_3 _Citation.Sf_category citations _Citation.Sf_framecode references_3 _Citation.Entry_ID 5908 _Citation.ID 4 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 11398456 _Citation.Full_citation ; Edmondson SP, Shriver JW. Methods Enzymol. 2001;334:129-45. ; _Citation.Title 'DNA binding proteins Sac7d and Sso7d from Sulfolobus.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Meth. Enzymol.' _Citation.Journal_name_full 'Methods in enzymology' _Citation.Journal_volume 334 _Citation.Journal_issue . _Citation.Journal_ASTM . _Citation.Journal_ISSN 0076-6879 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 129 _Citation.Page_last 145 _Citation.Year 2001 _Citation.Details . loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'S P' Edmondson S. P. . 5908 4 2 'J W' Shriver J. W. . 5908 4 stop_ save_ save_references_4 _Citation.Sf_category citations _Citation.Sf_framecode references_4 _Citation.Entry_ID 5908 _Citation.ID 5 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 11106160 _Citation.Full_citation ; Bedell JL, McCrary BS, Edmondson SP, Shriver JW. Protein Sci. 2000 Oct;9(10):1878-88. ; _Citation.Title 'The acid-induced folded state of Sac7d is the native state.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Protein Sci.' _Citation.Journal_name_full 'Protein science : a publication of the Protein Society' _Citation.Journal_volume 9 _Citation.Journal_issue 10 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0961-8368 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 1878 _Citation.Page_last 1888 _Citation.Year 2000 _Citation.Details ; Sac7d unfolds at low pH in the absence of salt, with the greatest extent of unfolding obtained at pH 2. We have previously shown that the acid unfolded protein is induced to refold by decreasing the pH to 0 or by addition of salt (McCrary BS, Bedell J. Edmondson SP, Shriver JW, 1998, J Mol Biol 276:203-224). Both near-ultraviolet circular dichroism spectra and ANS fluorescence enhancements indicate that the acid- and salt-induced folded states have a native fold and are not molten globular. 1H,15N heteronuclear single quantum coherence NMR spectra confirm that the native, acid-, and salt-induced folded states are essentially identical. The most significant differences in amide 1H and 15N chemical shifts are attributed to hydrogen bonding to titrating carboxyl side chains and through-bond inductive effects. The 1H NMR chemical shifts of protons affected by ring currents in the hydrophobic core of the acid- and salt-induced folded states are identical to those observed in the native. The radius of gyration of the acid-induced folded state at pH 0 is shown to be identical to that of the native state at pH 7 by small angle X-ray scattering. We conclude that acid-induced collapse of Sac7d does not lead to a molten globule but proceeds directly to the native state. The folding of Sac7d as a function of pH and anion concentration is summarized with a phase diagram that is similar to those observed for other proteins that undergo acid-induced folding except that the A-state is encompassed by the native state. These results demonstrate that formation of a molten globule is not a general property of proteins that are refolded by acid. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'J L' Bedell J. L. . 5908 5 2 'B S' McCrary B. S. . 5908 5 3 'S P' Edmondson S. P. . 5908 5 4 'J W' Shriver J. W. . 5908 5 stop_ save_ save_references_5 _Citation.Sf_category citations _Citation.Sf_framecode references_5 _Citation.Entry_ID 5908 _Citation.ID 6 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 11031116 _Citation.Full_citation ; Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH. J Mol Biol. 2000 Oct 27;303(3):395-403. ; _Citation.Title 'Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J. Mol. Biol.' _Citation.Journal_name_full 'Journal of molecular biology' _Citation.Journal_volume 303 _Citation.Journal_issue 3 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0022-2836 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 395 _Citation.Page_last 403 _Citation.Year 2000 _Citation.Details ; Sso7d and Sac7d are two small chromatin proteins from the hyperthermophilic archaeabacterium Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. The crystal structures of Sso7d-GTGATCGC, Sac7d-GTGATCGC and Sac7d-GTGATCAC have been determined and refined at 1.45 A, 2.2 A and 2.2 A, respectively, to investigate the DNA binding property of Sso7d/Sac7d in the presence of a T-G mismatch base-pair. Detailed structural analysis revealed that the intercalation site includes the T-G mismatch base-pair and Sso7d/Sac7d bind to that mismatch base-pair in a manner similar to regular DNA. In the Sso7d-GTGATCGC complex, a new inter-strand hydrogen bond between T2O4 and C14N4 is formed and well-order bridging water molecules are found. The results suggest that the less stable DNA stacking site involving a T-G mismatch may be a preferred site for protein side-chain intercalation. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 S Su S. . . 5908 6 2 'Y G' Gao Y. G. . 5908 6 3 H Robinson H. . . 5908 6 4 'Y C' Liaw Y. C. . 5908 6 5 'S P' Edmondson S. P. . 5908 6 6 'J W' Shriver J. W. . 5908 6 7 'A H' Wang A. H. . 5908 6 stop_ save_ save_references_6 _Citation.Sf_category citations _Citation.Sf_framecode references_6 _Citation.Entry_ID 5908 _Citation.ID 7 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 8520220 _Citation.Full_citation ; Delaglio, F. et al. J. Biomol. NMR 6, 277-293 (1995). ; _Citation.Title 'NMRPipe: a multidimensional spectral processing system based on UNIX pipes.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J. Biomol. NMR' _Citation.Journal_name_full 'Journal of biomolecular NMR' _Citation.Journal_volume 6 _Citation.Journal_issue 3 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0925-2738 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 277 _Citation.Page_last 293 _Citation.Year 1995 _Citation.Details ; The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 F Delaglio F. . . 5908 7 2 S Grzesiek S. . . 5908 7 3 'G W' Vuister G. W. . 5908 7 4 G Zhu G. . . 5908 7 5 J Pfeifer J. . . 5908 7 6 A Bax A. . . 5908 7 stop_ save_ save_references_7 _Citation.Sf_category citations _Citation.Sf_framecode references_7 _Citation.Entry_ID 5908 _Citation.ID 8 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 10343384 _Citation.Full_citation ; Hunenberger PH, McCammon JA. Biophys Chem. 1999 Apr 5;78(1-2):69-88. ; _Citation.Title 'Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Biophys. Chem.' _Citation.Journal_name_full 'Biophysical chemistry' _Citation.Journal_volume 78 _Citation.Journal_issue 1-2 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0301-4622 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 69 _Citation.Page_last 88 _Citation.Year 1999 _Citation.Details ; Ewald and related methods are nowadays routinely used in explicit-solvent simulations of biomolecules, although they impose an artificial periodicity in systems which are inherently non-periodic. The consequences of this approximation should be assessed, since they may crucially affect the reliability of computer simulations under Ewald boundary conditions. In the present study we use a method based on continuum electrostatics to investigate the nature and magnitude of possible periodicity-induced artifacts on the potentials of mean force for conformational equilibria in biomolecules. Three model systems and pathways are considered: polyalanine oligopeptides (unfolding), a DNA tetranucleotide (separation of the strands), and the protein Sac7d (conformations from a molecular dynamics simulation). Artificial periodicity may significantly affect these conformational equilibria, in each case stabilizing the most compact conformation of the biomolecule. Three factors enhance periodicity-induced artifacts: (i) a solvent of low dielectric permittivity; (ii) a solute size which is non-negligible compared to the size of the unit cell; and (iii) a non-neutral solute. Neither the neutrality of the solute nor the absence of charge pairs at distances exceeding half the edge of the unit cell do guarantee the absence of artifacts. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'P H' Hunenberger P. H. . 5908 8 2 'J A' McCammon J. A. . 5908 8 stop_ save_ save_references_8 _Citation.Sf_category citations _Citation.Sf_framecode references_8 _Citation.Entry_ID 5908 _Citation.ID 9 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 9917414 _Citation.Full_citation ; de Bakker PI, Hunenberger PH, McCammon JA. J Mol Biol. 1999 Jan 29;285(4):1811-30. ; _Citation.Title 'Molecular dynamics simulations of the hyperthermophilic protein sac7d from Sulfolobus acidocaldarius: contribution of salt bridges to thermostability.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J. Mol. Biol.' _Citation.Journal_name_full 'Journal of molecular biology' _Citation.Journal_volume 285 _Citation.Journal_issue 4 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0022-2836 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 1811 _Citation.Page_last 1830 _Citation.Year 1999 _Citation.Details ; Hyperthermophilic proteins often possess an increased number of surface salt bridges compared with their mesophilic homologues. However, salt bridges are generally thought to be of minor importance in protein stability at room temperature. In an effort to understand why this may no longer be true at elevated temperatures, we performed molecular dynamics simulations of the hyperthermophilic protein Sac7d at 300 K, 360 K, and 550 K. The three trajectories are stable on the nanosecond timescale, as evidenced by the analysis of several time-resolved properties. The simulations at 300 K and (to a lesser extent) 360 K are also compatible with nuclear Overhauser effect-derived distances. Raising the temperature from 300 K to 360 K results in a less favourable protein-solvent interaction energy, and a more favourable intraprotein interaction energy. Both effects are almost exclusively electrostatic in nature and dominated by contributions due to charged side-chains. The reduced solvation is due to a loss of spatial and orientational structure of water around charged side-chains, which is a consequence of the increased thermal motion in the solvent. The favourable change in the intraprotein Coulombic interaction energy is essentially due to the tightening of salt bridges. Assuming that charged side-chains are on average more distant from one another in the unfolded state than in the folded state, it follows that salt bridges may contribute to protein stability at elevated temperatures because (i) the solvation free energy of charged side-chains is more adversely affected in the unfolded state than in the folded state by an increase in temperature, and (ii) due to the tightening of salt bridges, unfolding implies a larger unfavourable increase in the intraprotein Coulombic energy at higher temperature. Possible causes for the unexpected stability of the protein at 550 K are also discussed. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'P I' 'de Bakker' P. I. . 5908 9 2 'P H' Hunenberger P. H. . 5908 9 3 'J A' McCammon J. A. . 5908 9 stop_ save_ save_references_10 _Citation.Sf_category citations _Citation.Sf_framecode references_10 _Citation.Entry_ID 5908 _Citation.ID 10 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 9731772 _Citation.Full_citation ; Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH. Nat Struct Biol. 1998 Sep;5(9):782-6. ; _Citation.Title 'The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Nat. Struct. Biol.' _Citation.Journal_name_full 'Nature structural biology' _Citation.Journal_volume 5 _Citation.Journal_issue 9 _Citation.Journal_ASTM . _Citation.Journal_ISSN 1072-8368 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 782 _Citation.Page_last 786 _Citation.Year 1998 _Citation.Details ; Sso7d and Sac7d are two small (approximately 7,000 Mr), but abundant, chromosomal proteins from the hyperthermophilic archaeabacteria Sulfolobus solfataricus and S. acidocaldarius respectively. These proteins have high thermal, acid and chemical stability. They bind DNA without marked sequence preference and increase the Tm of DNA by approximately 40 degrees C. Sso7d in complex with GTAATTAC and GCGT(iU)CGC + GCGAACGC was crystallized in different crystal lattices and the crystal structures were solved at high resolution. Sso7d binds in the minor groove of DNA and causes a single-step sharp kink in DNA (approximately 60 degrees) by the intercalation of the hydrophobic side chains of Val 26 and Met 29. The intercalation sites are different in the two complexes. Observations of this novel DNA binding mode in three independent crystal lattices indicate that it is not a function of crystal packing. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'Y G' Gao Y. G. . 5908 10 2 'S Y' Su S. Y. . 5908 10 3 H Robinson H. . . 5908 10 4 S Padmanabhan S. . . 5908 10 5 L Lim L. . . 5908 10 6 'B S' McCrary B. S. . 5908 10 7 'S P' Edmondson S. P. . 5908 10 8 'J W' Shriver J. W. . 5908 10 9 'A H' Wang A. H. . 5908 10 stop_ save_ save_references_11 _Citation.Sf_category citations _Citation.Sf_framecode references_11 _Citation.Entry_ID 5908 _Citation.ID 11 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 9515968 _Citation.Full_citation ; Robinson H, Gao YG, McCrary BS, Edmondson SP, Shriver JW, Wang AH. Nature. 1998 Mar 12;392(6672):202-5. ; _Citation.Title 'The hyperthermophile chromosomal protein Sac7d sharply kinks DNA.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev Nature _Citation.Journal_name_full Nature _Citation.Journal_volume 392 _Citation.Journal_issue 6672 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0028-0836 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 202 _Citation.Page_last 205 _Citation.Year 1998 _Citation.Details ; The proteins Sac7d and Sso7d belong to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius and S. solfactaricus, respectively. These proteins are extremely stable to heat, acid and chemical agents. Sac7d binds to DNA without any particular sequence preference and thereby increases its melting temperature by approximately 40 degrees C. We have now solved and refined the crystal structure of Sac7d in complex with two DNA sequences to high resolution. The structures are examples of a nonspecific DNA-binding protein bound to DNA, and reveal that Sac7d binds in the minor groove, causing a sharp kinking of the DNA helix that is more marked than that induced by any sequence-specific DNA-binding proteins. The kink results from the intercalation of specific hydrophobic side chains of Sac7d into the DNA structure, but without causing any significant distortion of the protein structure relative to the uncomplexed protein in solution. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 H Robinson H. . . 5908 11 2 'Y G' Gao Y. G. . 5908 11 3 'B S' McCrary B. S. . 5908 11 4 'S P' Edmondson S. P. . 5908 11 5 'J W' Shriver J. W. . 5908 11 6 'A H' Wang A. H. . 5908 11 stop_ save_ save_references_12 _Citation.Sf_category citations _Citation.Sf_framecode references_12 _Citation.Entry_ID 5908 _Citation.ID 12 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 9514720 _Citation.Full_citation ; McCrary BS, Bedell J, Edmondson SP, Shriver JW. J Mol Biol. 1998 Feb 13;276(1):203-24. ; _Citation.Title 'Linkage of protonation and anion binding to the folding of Sac7d.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J. Mol. Biol.' _Citation.Journal_name_full 'Journal of molecular biology' _Citation.Journal_volume 276 _Citation.Journal_issue 1 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0022-2836 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 203 _Citation.Page_last 224 _Citation.Year 1998 _Citation.Details ; The temperature, pH, and salt dependence of the folding of recombinant Sac7d from the hyperthermophile Sulfolobus acidocaldarius is mapped using multi-dimensional differential scanning calorimetry (DSC) and folding progress surfaces followed by circular dichroism. Linkage relations are derived to explain the observed dependencies, and it is shown that the data can be explained by the linkage of at least two protonation reactions and two anion binding sites to a two-state unfolding process. Circular dichroism spectra indicate that a native-like fold is stabilized at acid pH by anion binding. An apparent binding isotherm surface (folding progress versus pH and salt) is used to obtain intrinsic chloride binding constants as a function of pH for both sites. A saddle is predicted in the folding progress surface (progress versus temperature and pH) at low salt with a minimum near pH 2 and 20 degrees C with approximately 25% of the protein folded. The position of the saddle is sensitive to the intrinsic delta C degrees of unfolding and provides a third measure of delta C degrees independent of that obtained by a Kirchoff plot of DSC data and chemical denaturation. The observed enthalpy of unfolding approaches zero near the saddle making the unfolding largely invisible to DSC under these conditions. The linkage analysis demonstrates that the delta C degrees for unfolding obtained from a Kirchoff plot of DSC data should be distinguished from the intrinsic delta C degrees of unfolding. It is shown that the discrepancy between the free energy of unfolding for Sac7d obtained by DSC and that obtained by chemical denaturation may be explained by the linkage of protonation and anion binding to protein folding. The linkage analysis demonstrates the limitations of using the delta Hcal/ delta Hvh ratio an indication of two-state unfolding. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'B S' McCrary B. S. . 5908 12 2 J Bedell J. . . 5908 12 3 'S P' Edmondson S. P. . 5908 12 4 'J W' Shriver J. W. . 5908 12 stop_ save_ save_references_13 _Citation.Sf_category citations _Citation.Sf_framecode references_13 _Citation.Entry_ID 5908 _Citation.ID 13 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 9224936 _Citation.Full_citation ; Kulms D, Schafer G, Hahn U. Biol Chem. 1997 Jun;378(6):545-51. ; _Citation.Title 'Overproduction of Sac7d and Sac7e reveals only Sac7e to be a DNA-binding protein with ribonuclease activity from the extremophilic archaeon Sulfolobus acidocaldarius.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'Biol. Chem.' _Citation.Journal_name_full 'Biological chemistry' _Citation.Journal_volume 378 _Citation.Journal_issue 6 _Citation.Journal_ASTM . _Citation.Journal_ISSN 1431-6730 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 545 _Citation.Page_last 551 _Citation.Year 1997 _Citation.Details ; Genomic DNA from Sulfolobus acidocaldarius was screened using a degenerate oligodeoxyribonucleotide, derived from the sequence of 16 N-terminal amino acids from SaRD protein. SaRD protein was previously isolated in our laboratory and identified as a protein from S. acidocaldarius exhibiting ribonuclease activity as well as DNA-binding properties. On the basis of Southern hybridization analysis two genes from S. acidocaldarius have been cloned, sequenced and overproduced in Escherichia coli. The deduced amino acid sequences revealed that one gene encodes Sac7d and the other one Sac7e; two small, previously described basic proteins from S. acidocaldarius, and furthermore the N-termini of Sac7e and SaRD are identical. Northern blot analysis demonstrated that the genes are transcribed separately. After expression of sac7d and sac7e genes in E. coli it was shown that only recombinant Sac7e protein exhibits RNase activity and is catalytically indistinguishable from SaRD protein. Western blot analysis using a polyclonal antiserum raised against purified SaRD protein further confirmed that Sac7e and SaRD are identical proteins endowed with RNase activity and DNA-binding properties. A new RNA cleavage mechanism has to be postulated for Sac7e since, in contrast to common RNases (e.g. RNase A and T1), no histidines are present in the amino acid sequence. Differences between the very closely related 7 kDa proteins from two Sulfolobus strains converting DNA-binding proteins into RNases are pointed out and discussed, whereas substitutions of Glu by Gln (S. solfataricus) or by Lys (S. acidocaldarius) seem to be crucial. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 D Kulms D. . . 5908 13 2 G Schafer G. . . 5908 13 3 U Hahn U. . . 5908 13 stop_ save_ save_references_14 _Citation.Sf_category citations _Citation.Sf_framecode references_14 _Citation.Entry_ID 5908 _Citation.ID 14 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 8980686 _Citation.Full_citation ; McCrary BS, Edmondson SP, Shriver JW. J Mol Biol. 1996 Dec 13;264(4):784-805. ; _Citation.Title 'Hyperthermophile protein folding thermodynamics: differential scanning calorimetry and chemical denaturation of Sac7d.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J. Mol. Biol.' _Citation.Journal_name_full 'Journal of molecular biology' _Citation.Journal_volume 264 _Citation.Journal_issue 4 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0022-2836 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 784 _Citation.Page_last 805 _Citation.Year 1996 _Citation.Details ; Recombinant Sac7d protein from the thermoacidophile Sulfolobus acidocaldarius is shown to be stable towards acid, thermal and chemical denaturation. The protein maintains a compact native fold between pH 0 and 10 in 0.3 M KCl and 25 degrees C as indicated by near and far UV circular dichroism spectra. Thermal unfolding followed by differential scanning calorimetry (DSC) occurs as a reversible, two-state transition from pH 0 to 10, with a maximal Tm of 90.7 degrees C between pH 5 and 9. At pH 0 the protein unfolds with a Tm of 63.3 degrees C. Plots of the enthalpy of unfolding as a function of Tm are linear and yield an anomalously low delta Cp of 497 (+/-20) cal deg-1 mol-1 using the Kirchhoff relation. Guanidine hydrochloride and urea-induced chemical denaturation of Sac7d occur reversibly and can be followed by circular dichroism. Global non-linear regression of the chemical denaturation data constrained by DSC determined values for delta Hm and Tm yields a delta Cp of unfolding of 858 (+/-21) cal deg-1 mol-1. The higher delta Cp is in good agreement with that predicted from the buried polar and apolar surface areas using the NMR solution structure. It is similar to values reported for mesophile proteins of comparable size, indicating that the packing and change in solvent-accessible surface area on unfolding are not unusual. Similarly, guanidine hydrochloride and urea m-values are in good agreement with those expected for a protein of 66 residues. Possible explanations for the difference in delta Cp determined by application of the Kirchhoff relation to DSC data and that determined by the global fit are discussed. Protein stability curves defined by either delta Cp values are similar to those observed for small mesophile proteins. Although the protein is thermally stable, it is marginally stable thermodynamically with a free energy of unfolding of 1.6 (+/-0.1) kcal mol-1 at the growth temperature of 80 degrees C. The large number of potential ion pairs on the surface of this hyperthermophile protein do not result in an inordinate increase in stability. Post-translational modification, possibly lysine monomethylation, appears to be the single most important stabilizing factor that distinguishes the native hyperthermophile protein from small mesophile proteins. Additional stabilization in vivo is expected from compatible osmolytes (polyamines) and DNA-binding. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'B S' McCrary B. S. . 5908 14 2 'S P' Edmondson S. P. . 5908 14 3 'J W' Shriver J. W. . 5908 14 stop_ save_ save_references_15 _Citation.Sf_category citations _Citation.Sf_framecode references_15 _Citation.Entry_ID 5908 _Citation.ID 15 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 8672437 _Citation.Full_citation ; McAfee JG, Edmondson SP, Zegar I, Shriver JW. Biochemistry. 1996 Apr 2;35(13):4034-45. ; _Citation.Title 'Equilibrium DNA binding of Sac7d protein from the hyperthermophile Sulfolobus acidocaldarius: fluorescence and circular dichroism studies.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev Biochemistry _Citation.Journal_name_full Biochemistry _Citation.Journal_volume 35 _Citation.Journal_issue 13 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0006-2960 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 4034 _Citation.Page_last 4045 _Citation.Year 1996 _Citation.Details ; The thermodynamics of the binding of the Sac7d protein of Sulfolobus acidocaldarius to double-stranded DNA has been characterized using spectroscopic signals arising from both the protein and the DNA. Ligand binding density function analysis has been used to demonstrate that the fractional change in protein intrinsic tryptophan fluorescence quenching that occurs upon DNA binding is equal to the fraction of protein bound. Reverse titration data have been fit directly to the McGhee-von Hippel model [McGhee, J., & von Hippel, P. (1974) J. Mol. Biol. 86, 469-489] using nonlinear regression. Sac7d binds noncooperatively to poly(dGdC) x poly(dGdC) with an intrinsic affinity of 6.5 x 10(6) M(-1) and a site size of 4 base pairs in 1 mM KH2PO4 and 50 mM KC1 (pH 6.8). Some binding sequence preference is noted, with the binding to poly(dIdC) x poly(dIdC) over 10-fold stronger than to poly(DAdT) x poly(dAdT). The binding is largely driven by the polyelectrolyte effect and is consistent with a release of 4.4 monovalent cations from DNA upon complex formation or the formation of 5 ion pairs at the protein-DNA interface. Extrapolation of salt back-titration data to 1 M KC1 indicates a -2.2 kcal/mol nonelectrostatic contribution to the binding free energy. A van't Hoff analysis of poly(dGdC) x poly(dGdC) binding shows that the binding enthalpy is approximately zero and the process is entropically driven. The affinity decreases slightly between pH 5.4 and 8.0. There is no significant difference between the binding parameters of recombinant Sac7d and native Sac7 proteins, indicating that methylation of the native protein has no effect on the DNA binding function. The binding of Sac7d to various DNAs leads to a significant increase in the DNA long-wavelength circular dichroism (CD) band, the intensity of which shows a sigmoidal dependence on Sac7d concentration. The sigmoidal CD binding isotherm can be quantitatively modeled by a conformational transition in the DNA that is cooperatively induced when protein monomers are bound within a given number of base pairs, ranging from zero for poly(dIdC) x poly(dIdC) to 8 or less for poly(dAdG) x poly(dCdT). ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'J G' McAfee J. G. . 5908 15 2 'S P' Edmondson S. P. . 5908 15 3 I Zegar I. . . 5908 15 4 'J W' Shriver J. W. . 5908 15 stop_ save_ save_references_16 _Citation.Sf_category citations _Citation.Sf_framecode references_16 _Citation.Entry_ID 5908 _Citation.ID 16 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 7577913 _Citation.Full_citation ; Edmondson SP, Qiu L, Shriver JW. Biochemistry. 1995 Oct 17;34(41):13289-304. ; _Citation.Title 'Solution structure of the DNA-binding protein Sac7d from the hyperthermophile Sulfolobus acidocaldarius.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev Biochemistry _Citation.Journal_name_full Biochemistry _Citation.Journal_volume 34 _Citation.Journal_issue 41 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0006-2960 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 13289 _Citation.Page_last 13304 _Citation.Year 1995 _Citation.Details ; The Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius are a heterogeneous mixture of small, thermostable, nonspecific DNA-binding proteins. One of these proteins, Sac7d, has been overexpressed in Escherichia coli to provide a homogeneous preparation for structure, stability, and function studies. We present here essentially complete sequence-specific 1H NMR assignments for Sac7d, a delineation of secondary structural elements, and the high-resolution solution structure obtained from a full relaxation matrix refinement. The final structure provides an excellent fit to the NMR data with an NOE R-factor of 0.27 for backbone NOEs. The structure has a compact globular fold with 82% of the sequence involved in regular secondary structure: an antiparallel two-stranded beta-ribbon with a tight turn, followed by a short 3(10) helix, an antiparallel three-stranded beta-sheet, another short 3(10) helix, and finally four turns of alpha-helix. The amphipathic alpha-helix packs across the hydrophobic face of the three-stranded beta-sheet in an open-faced sandwich arrangement with at least one turn of the helix exposed beyond the sheet. The hydrophobic face of the beta-ribbon packs against a corner of the twisted beta-sheet. The single tryptophan responsible for the 88% fluorescence quenching upon DNA binding is exposed on the surface of the three-stranded beta-sheet. Lysines 5 and 7, whose monomethylation may be associated with enhanced thermostability, are highly solvent exposed along the inner edge of the two-stranded ribbon. The structure of Sac7d differs in many respects from that reported for the homologous native Sso7d [Baumann et al. (1994) Nature Struct. Biol. 1, 808] with a backbone RMSD greater than 3.0 A, largely due to the packing and length of the C-terminal alpha-helix which may be important in Sac7d DNA binding. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'S P' Edmondson S. P. . 5908 16 2 L Qiu L. . . 5908 16 3 'J W' Shriver J. W. . 5908 16 stop_ save_ save_references_17 _Citation.Sf_category citations _Citation.Sf_framecode references_17 _Citation.Entry_ID 5908 _Citation.ID 17 _Citation.Class 'reference citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 7632679 _Citation.Full_citation ; McAfee JG, Edmondson SP, Datta PK, Shriver JW, Gupta R. Biochemistry. 1995 Aug 8;34(31):10063-77. ; _Citation.Title 'Gene cloning, expression, and characterization of the Sac7 proteins from the hyperthermophile Sulfolobus acidocaldarius.' _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev Biochemistry _Citation.Journal_name_full Biochemistry _Citation.Journal_volume 34 _Citation.Journal_issue 31 _Citation.Journal_ASTM . _Citation.Journal_ISSN 0006-2960 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first 10063 _Citation.Page_last 10077 _Citation.Year 1995 _Citation.Details ; The genes for two Sac7 DNA-binding proteins, Sac7d and Sac7e, from the extremely thermophilic archaeon Sulfolobus acidocaldarius have been cloned into Escherichia coli and sequenced. The sac7d and sac7e open reading frames encode 66 amino acid (7608 Da) and 65 amino acid (7469 Da) proteins, respectively. Southern blots indicate that these are the only two Sac7 protein genes in S. acidocaldarius, each present as a single copy. Sac7a, b, and c proteins appear to be carboxy-terminal modified Sac7d species. The transcription initiation and termination regions of the sac7d and sac7e genes have been identified along with the promoter elements. Potential ribosome binding sites have been identified downstream of the initiator codons. The sac7d gene has been expressed in E. coli, and various physical properties of the recombinant protein have been compared with those of native Sac7. The UV absorbance spectra and extinction coefficients, the fluorescence excitation and emission spectra, the circular dichroism, and the two-dimensional double-quantum filtered 1H NMR spectra of the native and recombinant species are essentially identical, indicating essentially identical local and global folds. The recombinant and native proteins bind and stabilize double-stranded DNA with a site size of 3.5 base pairs and an intrinsic binding constant of 2 x 10(7) M-1 for poly[dGdC].poly[dGdC] in 0.01 M KH2PO4 at pH 7.0. The availability of the recombinant protein permits a direct comparison of the thermal stabilities of the methylated and unmethylated forms of the protein. Differential scanning calorimetry demonstrates that the native protein is extremely thermostable and unfolds reversibly at pH 6.0 with a Tm of approximately 100 degrees C, while the recombinant protein unfolds at 92.7 degrees C. ; loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.Entry_ID _Citation_author.Citation_ID 1 'J G' McAfee J. G. . 5908 17 2 'S P' Edmondson S. P. . 5908 17 3 'P K' Datta P. K. . 5908 17 4 'J W' Shriver J. W. . 5908 17 5 R Gupta R. . . 5908 17 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_system_Sac7d _Assembly.Sf_category assembly _Assembly.Sf_framecode system_Sac7d _Assembly.Entry_ID 5908 _Assembly.ID 1 _Assembly.Name 'Sac7d V30I monomer' _Assembly.BMRB_code . _Assembly.Number_of_components . _Assembly.Organic_ligands . _Assembly.Metal_ions . _Assembly.Non_standard_bonds . _Assembly.Ambiguous_conformational_states . _Assembly.Ambiguous_chem_comp_sites . _Assembly.Molecules_in_chemical_exchange . _Assembly.Paramagnetic no _Assembly.Thiol_state 'not present' _Assembly.Molecular_mass . _Assembly.Enzyme_commission_number . _Assembly.Details . _Assembly.DB_query_date . _Assembly.DB_query_revised_last_date . loop_ _Assembly_type.Type _Assembly_type.Entry_ID _Assembly_type.Assembly_ID monomer 5908 1 stop_ loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 'Sac7d V30I subunit 1' 1 $Sac7d . . . native . . . . . 5908 1 stop_ loop_ _Assembly_db_link.Author_supplied _Assembly_db_link.Database_code _Assembly_db_link.Accession_code _Assembly_db_link.Entry_mol_code _Assembly_db_link.Entry_mol_name _Assembly_db_link.Entry_experimental_method _Assembly_db_link.Entry_structure_resolution _Assembly_db_link.Entry_relation_type _Assembly_db_link.Entry_details _Assembly_db_link.Entry_ID _Assembly_db_link.Assembly_ID yes PDB 1SAP . . . . . . 5908 1 yes PDB 1AZP . . . . . . 5908 1 yes PDB 1AZQ . . . . . . 5908 1 yes PDB 1C8C . . . . . . 5908 1 yes PDB 1CA5 . . . . . . 5908 1 yes PDB 1CA6 . . . . . . 5908 1 stop_ loop_ _Assembly_common_name.Name _Assembly_common_name.Type _Assembly_common_name.Entry_ID _Assembly_common_name.Assembly_ID 'Sac7d V30I monomer' system 5908 1 Sac7d abbreviation 5908 1 stop_ loop_ _Assembly_bio_function.Biological_function _Assembly_bio_function.Entry_ID _Assembly_bio_function.Assembly_ID 'DNA-binding protein' 5908 1 'chromatin protein' 5908 1 'function unknown' 5908 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_Sac7d _Entity.Sf_category entity _Entity.Sf_framecode Sac7d _Entity.Entry_ID 5908 _Entity.ID 1 _Entity.BMRB_code . _Entity.Name Sac7d _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polypeptide(L) _Entity.Polymer_type_details . _Entity.Polymer_strand_ID . _Entity.Polymer_seq_one_letter_code_can ; MVKVKFKYKGEEKEVDTSKI KKVWRVGKMISFTYDDNGKT GRGAVSEKDAPKELLDMLAR AEREKK ; _Entity.Polymer_seq_one_letter_code ; MVKVKFKYKGEEKEVDTSKI KKVWRVGKMISFTYDDNGKT GRGAVSEKDAPKELLDMLAR AEREKK ; _Entity.Target_identifier . _Entity.Polymer_author_defined_seq . _Entity.Polymer_author_seq_details . _Entity.Ambiguous_conformational_states . _Entity.Ambiguous_chem_comp_sites . _Entity.Nstd_monomer . _Entity.Nstd_chirality . _Entity.Nstd_linkage . _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 66 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic . _Entity.Thiol_state 'not present' _Entity.Src_method . _Entity.Parent_entity_ID 1 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight 7623 _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details . _Entity.DB_query_date . _Entity.DB_query_revised_last_date 2015-01-28 loop_ _Entity_db_link.Ordinal _Entity_db_link.Author_supplied _Entity_db_link.Database_code _Entity_db_link.Accession_code _Entity_db_link.Entry_mol_code _Entity_db_link.Entry_mol_name _Entity_db_link.Entry_experimental_method _Entity_db_link.Entry_structure_resolution _Entity_db_link.Entry_relation_type _Entity_db_link.Entry_details _Entity_db_link.Chimera_segment_ID _Entity_db_link.Seq_query_to_submitted_percent _Entity_db_link.Seq_subject_length _Entity_db_link.Seq_identity _Entity_db_link.Seq_positive _Entity_db_link.Seq_homology_expectation_val _Entity_db_link.Seq_align_begin _Entity_db_link.Seq_align_end _Entity_db_link.Seq_difference_details _Entity_db_link.Seq_alignment_details _Entity_db_link.Entry_ID _Entity_db_link.Entity_ID 1 no BMRB 5905 . Sac7d . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 2 no PDB 1AZP . "Hyperthermophile Chromosomal Protein Sac7d Bound With Kinked Dna Duplex" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 3 no PDB 1AZQ . "Hyperthermophile Chromosomal Protein Sac7d Bound With Kinked Dna Duplex" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 4 no PDB 1CA5 . "Intercalation Site Of Hyperthermophile Chromosomal Protein Sso7dSAC7D Bound To Dna" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 5 no PDB 1CA6 . "Intercalation Site Of Hyperthermophile Chromosomal Protein Sso7dSAC7D Bound To Dna" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 6 no PDB 1SAP . "Hyperthermophile Protein, Relaxation Matrix Refinement Structure" . . . . . 98.48 66 98.46 100.00 3.83e-36 . . . . 5908 1 7 no PDB 1WD0 . "Crystal Structures Of The Hyperthermophilic Chromosomal Protein Sac7d In Complex With Dna Decamers" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 8 no PDB 1WD1 . "Crystal Structures Of The Hyperthermophilic Chromosomal Protein Sac7d In Complex With Dna Decamers" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 9 no PDB 1WTP . "Hyperthermophile Chromosomal Protein Sac7d Single Mutant M29f In Complex With Dna Gcga(Ubr)cgc" . . . . . 100.00 66 96.97 98.48 4.05e-36 . . . . 5908 1 10 no PDB 1WTQ . "Hyperthermophile Chromosomal Protein Sac7d Single Mutant M29f In Complex With Dna Gtaattac" . . . . . 100.00 66 96.97 98.48 4.05e-36 . . . . 5908 1 11 no PDB 1WTR . "Hyperthermophile Chromosomal Protein Sac7d Single Mutant M29a In Complex With Dna Gcgatcgc" . . . . . 100.00 66 96.97 98.48 4.61e-36 . . . . 5908 1 12 no PDB 1WTV . "Hyperthermophile Chromosomal Protein Sac7d Single Mutant M29a In Complex With Dna Gtaattac" . . . . . 100.00 66 96.97 98.48 4.61e-36 . . . . 5908 1 13 no PDB 1WTW . "Hyperthermophile Chromosomal Protein Sac7d Single Mutant V26a In Complex With Dna Gcgatcgc" . . . . . 100.00 66 96.97 98.48 1.98e-36 . . . . 5908 1 14 no PDB 1WTX . "Hyperthermophile Chromosomal Protein Sac7d Single Mutant V26a In Complex With Dna Gtaattac" . . . . . 100.00 66 96.97 98.48 1.98e-36 . . . . 5908 1 15 no PDB 1WVL . "Crystal Structure Of Multimeric Dna-Binding Protein Sac7d- Gcn4 With Dna Decamer" . . . . . 100.00 80 98.48 100.00 4.08e-37 . . . . 5908 1 16 no PDB 1XX8 . "Nmr Structure Of The W24a Mutant Of The Hyperthermophile Sac7d Protein" . . . . . 100.00 66 96.97 98.48 1.15e-35 . . . . 5908 1 17 no GB AAA80315 . "DNA-binding protein [Sulfolobus sp.]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 18 no GB AAY79492 . "conserved DNA-binding protein 7e [Sulfolobus acidocaldarius DSM 639]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 19 no GB AGE70041 . "DNA-binding protein 7e [Sulfolobus acidocaldarius N8]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 20 no GB AGE72316 . "DNA-binding protein 7e [Sulfolobus acidocaldarius Ron12/I]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 21 no GB AHC50588 . "DNA-binding protein [Sulfolobus acidocaldarius SUSAZ]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 22 no REF WP_011276993 . "DNA-binding protein [Sulfolobus acidocaldarius]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 23 no REF YP_007433189 . "DNA-binding protein 7e [Sulfolobus acidocaldarius N8]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 24 no REF YP_007435464 . "DNA-binding protein 7e [Sulfolobus acidocaldarius Ron12/I]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 25 no REF YP_254785 . "DNA-binding protein 7e [Sulfolobus acidocaldarius DSM 639]" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 26 no SP P13123 . "RecName: Full=DNA-binding protein 7d; AltName: Full=7 kDa DNA-binding protein d; AltName: Full=Sac7d; Contains: RecName: Full=D" . . . . . 100.00 66 98.48 100.00 5.48e-37 . . . . 5908 1 stop_ loop_ _Entity_common_name.Name _Entity_common_name.Type _Entity_common_name.Entry_ID _Entity_common_name.Entity_ID Sac7d common 5908 1 Sac7d abbreviation 5908 1 stop_ loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . MET . 5908 1 2 . VAL . 5908 1 3 . LYS . 5908 1 4 . VAL . 5908 1 5 . LYS . 5908 1 6 . PHE . 5908 1 7 . LYS . 5908 1 8 . TYR . 5908 1 9 . LYS . 5908 1 10 . GLY . 5908 1 11 . GLU . 5908 1 12 . GLU . 5908 1 13 . LYS . 5908 1 14 . GLU . 5908 1 15 . VAL . 5908 1 16 . ASP . 5908 1 17 . THR . 5908 1 18 . SER . 5908 1 19 . LYS . 5908 1 20 . ILE . 5908 1 21 . LYS . 5908 1 22 . LYS . 5908 1 23 . VAL . 5908 1 24 . TRP . 5908 1 25 . ARG . 5908 1 26 . VAL . 5908 1 27 . GLY . 5908 1 28 . LYS . 5908 1 29 . MET . 5908 1 30 . ILE . 5908 1 31 . SER . 5908 1 32 . PHE . 5908 1 33 . THR . 5908 1 34 . TYR . 5908 1 35 . ASP . 5908 1 36 . ASP . 5908 1 37 . ASN . 5908 1 38 . GLY . 5908 1 39 . LYS . 5908 1 40 . THR . 5908 1 41 . GLY . 5908 1 42 . ARG . 5908 1 43 . GLY . 5908 1 44 . ALA . 5908 1 45 . VAL . 5908 1 46 . SER . 5908 1 47 . GLU . 5908 1 48 . LYS . 5908 1 49 . ASP . 5908 1 50 . ALA . 5908 1 51 . PRO . 5908 1 52 . LYS . 5908 1 53 . GLU . 5908 1 54 . LEU . 5908 1 55 . LEU . 5908 1 56 . ASP . 5908 1 57 . MET . 5908 1 58 . LEU . 5908 1 59 . ALA . 5908 1 60 . ARG . 5908 1 61 . ALA . 5908 1 62 . GLU . 5908 1 63 . ARG . 5908 1 64 . GLU . 5908 1 65 . LYS . 5908 1 66 . LYS . 5908 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . MET 1 1 5908 1 . VAL 2 2 5908 1 . LYS 3 3 5908 1 . VAL 4 4 5908 1 . LYS 5 5 5908 1 . PHE 6 6 5908 1 . LYS 7 7 5908 1 . TYR 8 8 5908 1 . LYS 9 9 5908 1 . GLY 10 10 5908 1 . GLU 11 11 5908 1 . GLU 12 12 5908 1 . LYS 13 13 5908 1 . GLU 14 14 5908 1 . VAL 15 15 5908 1 . ASP 16 16 5908 1 . THR 17 17 5908 1 . SER 18 18 5908 1 . LYS 19 19 5908 1 . ILE 20 20 5908 1 . LYS 21 21 5908 1 . LYS 22 22 5908 1 . VAL 23 23 5908 1 . TRP 24 24 5908 1 . ARG 25 25 5908 1 . VAL 26 26 5908 1 . GLY 27 27 5908 1 . LYS 28 28 5908 1 . MET 29 29 5908 1 . ILE 30 30 5908 1 . SER 31 31 5908 1 . PHE 32 32 5908 1 . THR 33 33 5908 1 . TYR 34 34 5908 1 . ASP 35 35 5908 1 . ASP 36 36 5908 1 . ASN 37 37 5908 1 . GLY 38 38 5908 1 . LYS 39 39 5908 1 . THR 40 40 5908 1 . GLY 41 41 5908 1 . ARG 42 42 5908 1 . GLY 43 43 5908 1 . ALA 44 44 5908 1 . VAL 45 45 5908 1 . SER 46 46 5908 1 . GLU 47 47 5908 1 . LYS 48 48 5908 1 . ASP 49 49 5908 1 . ALA 50 50 5908 1 . PRO 51 51 5908 1 . LYS 52 52 5908 1 . GLU 53 53 5908 1 . LEU 54 54 5908 1 . LEU 55 55 5908 1 . ASP 56 56 5908 1 . MET 57 57 5908 1 . LEU 58 58 5908 1 . ALA 59 59 5908 1 . ARG 60 60 5908 1 . ALA 61 61 5908 1 . GLU 62 62 5908 1 . ARG 63 63 5908 1 . GLU 64 64 5908 1 . LYS 65 65 5908 1 . LYS 66 66 5908 1 stop_ save_ #################### # Natural source # #################### save_natural_source _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source _Entity_natural_src_list.Entry_ID 5908 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.Entity_chimera_segment_ID _Entity_natural_src.NCBI_taxonomy_ID _Entity_natural_src.Type _Entity_natural_src.Common _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Organism_name_common _Entity_natural_src.Organism_acronym _Entity_natural_src.ICTVdb_decimal_code _Entity_natural_src.Superkingdom _Entity_natural_src.Kingdom _Entity_natural_src.Genus _Entity_natural_src.Species _Entity_natural_src.Strain _Entity_natural_src.Variant _Entity_natural_src.Subvariant _Entity_natural_src.Organ _Entity_natural_src.Tissue _Entity_natural_src.Tissue_fraction _Entity_natural_src.Cell_line _Entity_natural_src.Cell_type _Entity_natural_src.ATCC_number _Entity_natural_src.Organelle _Entity_natural_src.Cellular_location _Entity_natural_src.Fragment _Entity_natural_src.Fraction _Entity_natural_src.Secretion _Entity_natural_src.Plasmid _Entity_natural_src.Plasmid_details _Entity_natural_src.Gene_mnemonic _Entity_natural_src.Dev_stage _Entity_natural_src.Details _Entity_natural_src.Citation_ID _Entity_natural_src.Citation_label _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $Sac7d . 2285 . . 'Sulfolobus acidocaldarius' 'Sulfolobus acidocaldarius Brock et al.' . . Archaea . Sulfolobus acidocaldarius . . . . . . . . . . . . . . . . . . . . . 5908 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source _Entity_experimental_src_list.Entry_ID 5908 _Entity_experimental_src_list.ID 1 loop_ _Entity_experimental_src.ID _Entity_experimental_src.Entity_ID _Entity_experimental_src.Entity_label _Entity_experimental_src.Entity_chimera_segment_ID _Entity_experimental_src.Production_method _Entity_experimental_src.Host_org_scientific_name _Entity_experimental_src.Host_org_name_common _Entity_experimental_src.Host_org_details _Entity_experimental_src.Host_org_NCBI_taxonomy_ID _Entity_experimental_src.Host_org_genus _Entity_experimental_src.Host_org_species _Entity_experimental_src.Host_org_strain _Entity_experimental_src.Host_org_variant _Entity_experimental_src.Host_org_subvariant _Entity_experimental_src.Host_org_organ _Entity_experimental_src.Host_org_tissue _Entity_experimental_src.Host_org_tissue_fraction _Entity_experimental_src.Host_org_cell_line _Entity_experimental_src.Host_org_cell_type _Entity_experimental_src.Host_org_cellular_location _Entity_experimental_src.Host_org_organelle _Entity_experimental_src.Host_org_gene _Entity_experimental_src.Host_org_culture_collection _Entity_experimental_src.Host_org_ATCC_number _Entity_experimental_src.Vector_type _Entity_experimental_src.PDBview_host_org_vector_name _Entity_experimental_src.PDBview_plasmid_name _Entity_experimental_src.Vector_name _Entity_experimental_src.Vector_details _Entity_experimental_src.Vendor_name _Entity_experimental_src.Host_org_dev_stage _Entity_experimental_src.Details _Entity_experimental_src.Citation_ID _Entity_experimental_src.Citation_label _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $Sac7d . 'recombinant technology' . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5908 1 stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_Sac7d_V30I _Sample.Sf_category sample _Sample.Sf_framecode Sac7d_V30I _Sample.Entry_ID 5908 _Sample.ID 1 _Sample.Type solution _Sample.Sub_type . _Sample.Details . _Sample.Aggregate_sample_number . _Sample.Solvent_system . _Sample.Preparation_date . _Sample.Preparation_expiration_date . _Sample.Polycrystallization_protocol . _Sample.Single_crystal_protocol . _Sample.Crystal_grow_apparatus . _Sample.Crystal_grow_atmosphere . _Sample.Crystal_grow_details . _Sample.Crystal_grow_method . _Sample.Crystal_grow_method_cit_ID . _Sample.Crystal_grow_pH . _Sample.Crystal_grow_pH_range . _Sample.Crystal_grow_pressure . _Sample.Crystal_grow_pressure_esd . _Sample.Crystal_grow_seeding . _Sample.Crystal_grow_seeding_cit_ID . _Sample.Crystal_grow_temp . _Sample.Crystal_grow_temp_details . _Sample.Crystal_grow_temp_esd . _Sample.Crystal_grow_time . _Sample.Oriented_sample_prep_protocol . _Sample.Lyophilization_cryo_protectant . _Sample.Storage_protocol . loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Assembly_ID _Sample_component.Assembly_label _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Product_ID _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_min _Sample_component.Concentration_val_max _Sample_component.Concentration_val_units _Sample_component.Concentration_val_err _Sample_component.Vendor _Sample_component.Vendor_product_name _Sample_component.Vendor_product_code _Sample_component.Entry_ID _Sample_component.Sample_ID 1 Sac7d '[U-98% 15N]' . . 1 $Sac7d . . 1.18 1 1.5 mM . . . . 5908 1 2 KCl . . . . . . . 0.3 . . M . . . . 5908 1 3 H2O . . . . . . . 90 . . % . . . . 5908 1 4 D2O . . . . . . . 10 . . % . . . . 5908 1 5 DSS . . . . . . . 100 . . uM . . . . 5908 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conds _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conds _Sample_condition_list.Entry_ID 5908 _Sample_condition_list.ID 1 _Sample_condition_list.Details . loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_err _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID pH 4.06 0.1 n/a 5908 1 temperature 303 1 K 5908 1 stop_ save_ ############################ # Computer software used # ############################ save_NMRPipe _Software.Sf_category software _Software.Sf_framecode NMRPipe _Software.Entry_ID 5908 _Software.ID 1 _Software.Name NMRPipe _Software.Version . _Software.Details . loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'data processing' 5908 1 transformation 5908 1 referencing 5908 1 stop_ save_ save_NMRView _Software.Sf_category software _Software.Sf_framecode NMRView _Software.Entry_ID 5908 _Software.ID 2 _Software.Name NMRView _Software.Version 5 _Software.Details . loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'sequential assignments' 5908 2 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_1 _NMR_spectrometer.Entry_ID 5908 _NMR_spectrometer.ID 1 _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Varian _NMR_spectrometer.Model VXR-S _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 500 save_ save_NMR_spectrometer_2 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_2 _NMR_spectrometer.Entry_ID 5908 _NMR_spectrometer.ID 2 _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Varian _NMR_spectrometer.Model INOVA _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 500 save_ save_NMR_spectrometer_3 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_3 _NMR_spectrometer.Entry_ID 5908 _NMR_spectrometer.ID 3 _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Varian _NMR_spectrometer.Model INOVA _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 800 save_ save_spectrometer_list _NMR_spectrometer_list.Sf_category NMR_spectrometer_list _NMR_spectrometer_list.Sf_framecode spectrometer_list _NMR_spectrometer_list.Entry_ID 5908 _NMR_spectrometer_list.ID 1 loop_ _NMR_spectrometer_view.ID _NMR_spectrometer_view.Name _NMR_spectrometer_view.Manufacturer _NMR_spectrometer_view.Model _NMR_spectrometer_view.Serial_number _NMR_spectrometer_view.Field_strength _NMR_spectrometer_view.Details _NMR_spectrometer_view.Citation_ID _NMR_spectrometer_view.Citation_label _NMR_spectrometer_view.Entry_ID _NMR_spectrometer_view.NMR_spectrometer_list_ID 1 NMR_spectrometer_1 Varian VXR-S . 500 . . . 5908 1 2 NMR_spectrometer_2 Varian INOVA . 500 . . . 5908 1 3 NMR_spectrometer_3 Varian INOVA . 800 . . . 5908 1 stop_ save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID 5908 _Experiment_list.ID 1 _Experiment_list.Details . loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_flag _Experiment.NMR_spec_expt_ID _Experiment.NMR_spec_expt_label _Experiment.MS_expt_ID _Experiment.MS_expt_label _Experiment.SAXS_expt_ID _Experiment.SAXS_expt_label _Experiment.FRET_expt_ID _Experiment.FRET_expt_label _Experiment.EMR_expt_ID _Experiment.EMR_expt_label _Experiment.Sample_ID _Experiment.Sample_label _Experiment.Sample_state _Experiment.Sample_volume _Experiment.Sample_volume_units _Experiment.Sample_condition_list_ID _Experiment.Sample_condition_list_label _Experiment.Sample_spinning_rate _Experiment.Sample_angle _Experiment.NMR_tube_type _Experiment.NMR_spectrometer_ID _Experiment.NMR_spectrometer_label _Experiment.NMR_spectrometer_probe_ID _Experiment.NMR_spectrometer_probe_label _Experiment.NMR_spectral_processing_ID _Experiment.NMR_spectral_processing_label _Experiment.Mass_spectrometer_ID _Experiment.Mass_spectrometer_label _Experiment.Xray_instrument_ID _Experiment.Xray_instrument_label _Experiment.Fluorescence_instrument_ID _Experiment.Fluorescence_instrument_label _Experiment.EMR_instrument_ID _Experiment.EMR_instrument_label _Experiment.Chromatographic_system_ID _Experiment.Chromatographic_system_label _Experiment.Chromatographic_column_ID _Experiment.Chromatographic_column_label _Experiment.Entry_ID _Experiment.Experiment_list_ID 1 '1H,15N HSQC' . . . . . . . . . . . 1 $Sac7d_V30I . . . 1 $sample_conds . . . . . . . . . . . . . . . . . . . . . 5908 1 2 '3D HSQC-TOCSY' . . . . . . . . . . . 1 $Sac7d_V30I . . . 1 $sample_conds . . . . . . . . . . . . . . . . . . . . . 5908 1 3 '3D HSQC-NOESY' . . . . . . . . . . . 1 $Sac7d_V30I . . . 1 $sample_conds . . . . . . . . . . . . . . . . . . . . . 5908 1 stop_ save_ save_NMR_spec_expt__0_1 _NMR_spec_expt.Sf_category NMR_spectrometer_expt _NMR_spec_expt.Sf_framecode NMR_spec_expt__0_1 _NMR_spec_expt.Entry_ID 5908 _NMR_spec_expt.ID 1 _NMR_spec_expt.Name '1H,15N HSQC' _NMR_spec_expt.Type . _NMR_spec_expt.Sample_volume . _NMR_spec_expt.Sample_volume_units . _NMR_spec_expt.NMR_tube_type . _NMR_spec_expt.Sample_spinning_rate . _NMR_spec_expt.Sample_angle . _NMR_spec_expt.NMR_spectrometer_ID . _NMR_spec_expt.NMR_spectrometer_label . _NMR_spec_expt.NMR_spectrometer_probe_ID . _NMR_spec_expt.NMR_spectrometer_probe_label . _NMR_spec_expt.Carrier_freq_switch_time . _NMR_spec_expt.Software_ID . _NMR_spec_expt.Software_label . _NMR_spec_expt.Method_ID . _NMR_spec_expt.Method_label . _NMR_spec_expt.Pulse_seq_accession_BMRB_code . _NMR_spec_expt.Details . save_ save_NMR_spec_expt__0_2 _NMR_spec_expt.Sf_category NMR_spectrometer_expt _NMR_spec_expt.Sf_framecode NMR_spec_expt__0_2 _NMR_spec_expt.Entry_ID 5908 _NMR_spec_expt.ID 2 _NMR_spec_expt.Name '3D HSQC-TOCSY' _NMR_spec_expt.Type . _NMR_spec_expt.Sample_volume . _NMR_spec_expt.Sample_volume_units . _NMR_spec_expt.NMR_tube_type . _NMR_spec_expt.Sample_spinning_rate . _NMR_spec_expt.Sample_angle . _NMR_spec_expt.NMR_spectrometer_ID . _NMR_spec_expt.NMR_spectrometer_label . _NMR_spec_expt.NMR_spectrometer_probe_ID . _NMR_spec_expt.NMR_spectrometer_probe_label . _NMR_spec_expt.Carrier_freq_switch_time . _NMR_spec_expt.Software_ID . _NMR_spec_expt.Software_label . _NMR_spec_expt.Method_ID . _NMR_spec_expt.Method_label . _NMR_spec_expt.Pulse_seq_accession_BMRB_code . _NMR_spec_expt.Details . save_ save_NMR_spec_expt__0_3 _NMR_spec_expt.Sf_category NMR_spectrometer_expt _NMR_spec_expt.Sf_framecode NMR_spec_expt__0_3 _NMR_spec_expt.Entry_ID 5908 _NMR_spec_expt.ID 3 _NMR_spec_expt.Name '3D HSQC-NOESY' _NMR_spec_expt.Type . _NMR_spec_expt.Sample_volume . _NMR_spec_expt.Sample_volume_units . _NMR_spec_expt.NMR_tube_type . _NMR_spec_expt.Sample_spinning_rate . _NMR_spec_expt.Sample_angle . _NMR_spec_expt.NMR_spectrometer_ID . _NMR_spec_expt.NMR_spectrometer_label . _NMR_spec_expt.NMR_spectrometer_probe_ID . _NMR_spec_expt.NMR_spectrometer_probe_label . _NMR_spec_expt.Carrier_freq_switch_time . _NMR_spec_expt.Software_ID . _NMR_spec_expt.Software_label . _NMR_spec_expt.Method_ID . _NMR_spec_expt.Method_label . _NMR_spec_expt.Pulse_seq_accession_BMRB_code . _NMR_spec_expt.Details . save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chemical_shift_reference _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chemical_shift_reference _Chem_shift_reference.Entry_ID 5908 _Chem_shift_reference.ID 1 _Chem_shift_reference.Details . loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Concentration_val _Chem_shift_ref.Concentration_units _Chem_shift_ref.Solvent _Chem_shift_ref.Rank _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_method _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.External_ref_loc _Chem_shift_ref.External_ref_sample_geometry _Chem_shift_ref.External_ref_axis _Chem_shift_ref.Indirect_shift_ratio_cit_ID _Chem_shift_ref.Indirect_shift_ratio_cit_label _Chem_shift_ref.Ref_correction_type _Chem_shift_ref.Correction_val _Chem_shift_ref.Correction_val_cit_ID _Chem_shift_ref.Correction_val_cit_label _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 DSS 'methyl protons' . . . . ppm 0.0 internal direct 1.0 . . . . . . . . . 5908 1 N 15 DSS 'methyl protons' . . . . ppm 0.0 . indirect 0.101329118 . . . . . . . . . 5908 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_V30I_shift_set_1 _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode V30I_shift_set_1 _Assigned_chem_shift_list.Entry_ID 5908 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conds _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chemical_shift_reference _Assigned_chem_shift_list.Chem_shift_1H_err . _Assigned_chem_shift_list.Chem_shift_13C_err . _Assigned_chem_shift_list.Chem_shift_15N_err . _Assigned_chem_shift_list.Chem_shift_31P_err . _Assigned_chem_shift_list.Chem_shift_2H_err . _Assigned_chem_shift_list.Chem_shift_19F_err . _Assigned_chem_shift_list.Error_derivation_method . _Assigned_chem_shift_list.Details . _Assigned_chem_shift_list.Text_data_format . _Assigned_chem_shift_list.Text_data . loop_ _Chem_shift_experiment.Experiment_ID _Chem_shift_experiment.Experiment_name _Chem_shift_experiment.Sample_ID _Chem_shift_experiment.Sample_label _Chem_shift_experiment.Sample_state _Chem_shift_experiment.Entry_ID _Chem_shift_experiment.Assigned_chem_shift_list_ID . . 1 $Sac7d_V30I . 5908 1 stop_ loop_ _Atom_chem_shift.ID _Atom_chem_shift.Assembly_atom_ID _Atom_chem_shift.Entity_assembly_ID _Atom_chem_shift.Entity_ID _Atom_chem_shift.Comp_index_ID _Atom_chem_shift.Seq_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Val_err _Atom_chem_shift.Assign_fig_of_merit _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Occupancy _Atom_chem_shift.Resonance_ID _Atom_chem_shift.Auth_entity_assembly_ID _Atom_chem_shift.Auth_asym_ID _Atom_chem_shift.Auth_seq_ID _Atom_chem_shift.Auth_comp_ID _Atom_chem_shift.Auth_atom_ID _Atom_chem_shift.Details _Atom_chem_shift.Entry_ID _Atom_chem_shift.Assigned_chem_shift_list_ID 1 . 1 1 2 2 VAL H H 1 8.675 0.01 . 1 . . . . . . . . 5908 1 2 . 1 1 2 2 VAL N N 15 123.971 0.05 . 1 . . . . . . . . 5908 1 3 . 1 1 3 3 LYS H H 1 8.424 0.01 . 1 . . . . . . . . 5908 1 4 . 1 1 3 3 LYS N N 15 123.876 0.05 . 1 . . . . . . . . 5908 1 5 . 1 1 4 4 VAL H H 1 8.876 0.01 . 1 . . . . . . . . 5908 1 6 . 1 1 4 4 VAL N N 15 121.556 0.05 . 1 . . . . . . . . 5908 1 7 . 1 1 5 5 LYS H H 1 8.494 0.01 . 1 . . . . . . . . 5908 1 8 . 1 1 5 5 LYS N N 15 127.835 0.05 . 1 . . . . . . . . 5908 1 9 . 1 1 6 6 PHE H H 1 8.675 0.01 . 1 . . . . . . . . 5908 1 10 . 1 1 6 6 PHE N N 15 120.258 0.05 . 1 . . . . . . . . 5908 1 11 . 1 1 7 7 LYS H H 1 8.708 0.01 . 1 . . . . . . . . 5908 1 12 . 1 1 7 7 LYS N N 15 119.294 0.05 . 1 . . . . . . . . 5908 1 13 . 1 1 8 8 TYR H H 1 8.989 0.01 . 1 . . . . . . . . 5908 1 14 . 1 1 8 8 TYR N N 15 124.941 0.05 . 1 . . . . . . . . 5908 1 15 . 1 1 9 9 LYS H H 1 9.155 0.01 . 1 . . . . . . . . 5908 1 16 . 1 1 9 9 LYS N N 15 127.976 0.05 . 1 . . . . . . . . 5908 1 17 . 1 1 10 10 GLY H H 1 8.476 0.01 . 1 . . . . . . . . 5908 1 18 . 1 1 10 10 GLY N N 15 103.500 0.05 . 1 . . . . . . . . 5908 1 19 . 1 1 11 11 GLU H H 1 7.868 0.01 . 1 . . . . . . . . 5908 1 20 . 1 1 11 11 GLU N N 15 119.996 0.05 . 1 . . . . . . . . 5908 1 21 . 1 1 12 12 GLU H H 1 8.689 0.01 . 1 . . . . . . . . 5908 1 22 . 1 1 12 12 GLU N N 15 123.474 0.05 . 1 . . . . . . . . 5908 1 23 . 1 1 13 13 LYS H H 1 8.848 0.01 . 1 . . . . . . . . 5908 1 24 . 1 1 13 13 LYS N N 15 126.533 0.05 . 1 . . . . . . . . 5908 1 25 . 1 1 14 14 GLU H H 1 7.932 0.01 . 1 . . . . . . . . 5908 1 26 . 1 1 14 14 GLU N N 15 116.671 0.05 . 1 . . . . . . . . 5908 1 27 . 1 1 15 15 VAL H H 1 8.651 0.01 . 1 . . . . . . . . 5908 1 28 . 1 1 15 15 VAL N N 15 121.011 0.05 . 1 . . . . . . . . 5908 1 29 . 1 1 16 16 ASP H H 1 8.540 0.01 . 1 . . . . . . . . 5908 1 30 . 1 1 16 16 ASP N N 15 127.101 0.05 . 1 . . . . . . . . 5908 1 31 . 1 1 17 17 THR H H 1 8.790 0.01 . 1 . . . . . . . . 5908 1 32 . 1 1 17 17 THR N N 15 116.111 0.05 . 1 . . . . . . . . 5908 1 33 . 1 1 18 18 SER H H 1 8.619 0.01 . 1 . . . . . . . . 5908 1 34 . 1 1 18 18 SER N N 15 116.507 0.05 . 1 . . . . . . . . 5908 1 35 . 1 1 19 19 LYS H H 1 7.971 0.01 . 1 . . . . . . . . 5908 1 36 . 1 1 19 19 LYS N N 15 119.267 0.05 . 1 . . . . . . . . 5908 1 37 . 1 1 20 20 ILE H H 1 7.274 0.01 . 1 . . . . . . . . 5908 1 38 . 1 1 20 20 ILE N N 15 120.854 0.05 . 1 . . . . . . . . 5908 1 39 . 1 1 21 21 LYS H H 1 8.866 0.01 . 1 . . . . . . . . 5908 1 40 . 1 1 21 21 LYS N N 15 127.832 0.05 . 1 . . . . . . . . 5908 1 41 . 1 1 22 22 LYS H H 1 7.470 0.01 . 1 . . . . . . . . 5908 1 42 . 1 1 22 22 LYS N N 15 119.896 0.05 . 1 . . . . . . . . 5908 1 43 . 1 1 23 23 VAL H H 1 8.179 0.01 . 1 . . . . . . . . 5908 1 44 . 1 1 23 23 VAL N N 15 118.804 0.05 . 1 . . . . . . . . 5908 1 45 . 1 1 24 24 TRP H H 1 9.261 0.01 . 1 . . . . . . . . 5908 1 46 . 1 1 24 24 TRP N N 15 125.193 0.05 . 1 . . . . . . . . 5908 1 47 . 1 1 24 24 TRP NE1 N 15 129.279 0.05 . 1 . . . . . . . . 5908 1 48 . 1 1 24 24 TRP HE1 H 1 10.074 0.01 . 2 . . . . . . . . 5908 1 49 . 1 1 25 25 ARG H H 1 8.784 0.01 . 1 . . . . . . . . 5908 1 50 . 1 1 25 25 ARG N N 15 120.386 0.05 . 1 . . . . . . . . 5908 1 51 . 1 1 26 26 VAL H H 1 8.615 0.01 . 1 . . . . . . . . 5908 1 52 . 1 1 26 26 VAL N N 15 126.037 0.05 . 1 . . . . . . . . 5908 1 53 . 1 1 27 27 GLY H H 1 9.121 0.01 . 1 . . . . . . . . 5908 1 54 . 1 1 27 27 GLY N N 15 118.323 0.05 . 1 . . . . . . . . 5908 1 55 . 1 1 28 28 LYS H H 1 8.884 0.01 . 1 . . . . . . . . 5908 1 56 . 1 1 28 28 LYS N N 15 126.621 0.05 . 1 . . . . . . . . 5908 1 57 . 1 1 29 29 MET H H 1 8.175 0.01 . 1 . . . . . . . . 5908 1 58 . 1 1 29 29 MET N N 15 118.050 0.05 . 1 . . . . . . . . 5908 1 59 . 1 1 30 30 ILE H H 1 9.280 0.01 . 1 . . . . . . . . 5908 1 60 . 1 1 30 30 ILE N N 15 123.644 0.05 . 1 . . . . . . . . 5908 1 61 . 1 1 31 31 SER H H 1 8.717 0.01 . 1 . . . . . . . . 5908 1 62 . 1 1 31 31 SER N N 15 122.907 0.05 . 1 . . . . . . . . 5908 1 63 . 1 1 32 32 PHE H H 1 7.586 0.01 . 1 . . . . . . . . 5908 1 64 . 1 1 32 32 PHE N N 15 114.592 0.05 . 1 . . . . . . . . 5908 1 65 . 1 1 33 33 THR H H 1 8.926 0.01 . 1 . . . . . . . . 5908 1 66 . 1 1 33 33 THR N N 15 109.064 0.05 . 1 . . . . . . . . 5908 1 67 . 1 1 34 34 TYR H H 1 8.612 0.01 . 1 . . . . . . . . 5908 1 68 . 1 1 34 34 TYR N N 15 116.158 0.05 . 1 . . . . . . . . 5908 1 69 . 1 1 35 35 ASP H H 1 8.572 0.01 . 1 . . . . . . . . 5908 1 70 . 1 1 35 35 ASP N N 15 119.438 0.05 . 1 . . . . . . . . 5908 1 71 . 1 1 36 36 ASP H H 1 8.918 0.01 . 1 . . . . . . . . 5908 1 72 . 1 1 36 36 ASP N N 15 127.105 0.05 . 1 . . . . . . . . 5908 1 73 . 1 1 37 37 ASN H H 1 8.689 0.01 . 1 . . . . . . . . 5908 1 74 . 1 1 37 37 ASN N N 15 120.447 0.05 . 1 . . . . . . . . 5908 1 75 . 1 1 37 37 ASN ND2 N 15 113.132 0.05 . 1 . . . . . . . . 5908 1 76 . 1 1 37 37 ASN HD21 H 1 7.590 0.01 . 2 . . . . . . . . 5908 1 77 . 1 1 37 37 ASN HD22 H 1 6.905 0.01 . 2 . . . . . . . . 5908 1 78 . 1 1 38 38 GLY H H 1 8.795 0.01 . 1 . . . . . . . . 5908 1 79 . 1 1 38 38 GLY N N 15 106.152 0.05 . 1 . . . . . . . . 5908 1 80 . 1 1 39 39 LYS H H 1 7.489 0.01 . 1 . . . . . . . . 5908 1 81 . 1 1 39 39 LYS N N 15 120.117 0.05 . 1 . . . . . . . . 5908 1 82 . 1 1 40 40 THR H H 1 8.612 0.01 . 1 . . . . . . . . 5908 1 83 . 1 1 40 40 THR N N 15 118.351 0.05 . 1 . . . . . . . . 5908 1 84 . 1 1 41 41 GLY H H 1 8.528 0.01 . 1 . . . . . . . . 5908 1 85 . 1 1 41 41 GLY N N 15 115.315 0.05 . 1 . . . . . . . . 5908 1 86 . 1 1 42 42 ARG H H 1 7.720 0.01 . 1 . . . . . . . . 5908 1 87 . 1 1 42 42 ARG N N 15 117.967 0.05 . 1 . . . . . . . . 5908 1 88 . 1 1 43 43 GLY H H 1 7.725 0.01 . 1 . . . . . . . . 5908 1 89 . 1 1 43 43 GLY N N 15 107.320 0.05 . 1 . . . . . . . . 5908 1 90 . 1 1 44 44 ALA H H 1 6.731 0.01 . 1 . . . . . . . . 5908 1 91 . 1 1 44 44 ALA N N 15 117.474 0.05 . 1 . . . . . . . . 5908 1 92 . 1 1 45 45 VAL H H 1 9.040 0.01 . 1 . . . . . . . . 5908 1 93 . 1 1 45 45 VAL N N 15 116.438 0.05 . 1 . . . . . . . . 5908 1 94 . 1 1 46 46 SER H H 1 9.026 0.01 . 1 . . . . . . . . 5908 1 95 . 1 1 46 46 SER N N 15 121.484 0.05 . 1 . . . . . . . . 5908 1 96 . 1 1 47 47 GLU H H 1 8.803 0.01 . 1 . . . . . . . . 5908 1 97 . 1 1 47 47 GLU N N 15 123.859 0.05 . 1 . . . . . . . . 5908 1 98 . 1 1 48 48 LYS H H 1 8.109 0.01 . 1 . . . . . . . . 5908 1 99 . 1 1 48 48 LYS N N 15 116.159 0.05 . 1 . . . . . . . . 5908 1 100 . 1 1 49 49 ASP H H 1 7.562 0.01 . 1 . . . . . . . . 5908 1 101 . 1 1 49 49 ASP N N 15 116.636 0.05 . 1 . . . . . . . . 5908 1 102 . 1 1 50 50 ALA H H 1 7.430 0.01 . 1 . . . . . . . . 5908 1 103 . 1 1 50 50 ALA N N 15 124.408 0.05 . 1 . . . . . . . . 5908 1 104 . 1 1 52 52 LYS H H 1 8.987 0.01 . 1 . . . . . . . . 5908 1 105 . 1 1 52 52 LYS N N 15 125.234 0.05 . 1 . . . . . . . . 5908 1 106 . 1 1 53 53 GLU H H 1 9.543 0.01 . 1 . . . . . . . . 5908 1 107 . 1 1 53 53 GLU N N 15 116.264 0.05 . 1 . . . . . . . . 5908 1 108 . 1 1 54 54 LEU H H 1 7.282 0.01 . 1 . . . . . . . . 5908 1 109 . 1 1 54 54 LEU N N 15 117.000 0.05 . 1 . . . . . . . . 5908 1 110 . 1 1 55 55 LEU H H 1 7.419 0.01 . 1 . . . . . . . . 5908 1 111 . 1 1 55 55 LEU N N 15 119.179 0.05 . 1 . . . . . . . . 5908 1 112 . 1 1 56 56 ASP H H 1 8.783 0.01 . 1 . . . . . . . . 5908 1 113 . 1 1 56 56 ASP N N 15 120.603 0.05 . 1 . . . . . . . . 5908 1 114 . 1 1 57 57 MET H H 1 7.627 0.01 . 1 . . . . . . . . 5908 1 115 . 1 1 57 57 MET N N 15 119.752 0.05 . 1 . . . . . . . . 5908 1 116 . 1 1 58 58 LEU H H 1 7.966 0.01 . 1 . . . . . . . . 5908 1 117 . 1 1 58 58 LEU N N 15 121.198 0.05 . 1 . . . . . . . . 5908 1 118 . 1 1 59 59 ALA H H 1 8.044 0.01 . 1 . . . . . . . . 5908 1 119 . 1 1 59 59 ALA N N 15 120.974 0.05 . 1 . . . . . . . . 5908 1 120 . 1 1 60 60 ARG H H 1 7.831 0.01 . 1 . . . . . . . . 5908 1 121 . 1 1 60 60 ARG N N 15 117.114 0.05 . 1 . . . . . . . . 5908 1 122 . 1 1 61 61 ALA H H 1 7.959 0.01 . 1 . . . . . . . . 5908 1 123 . 1 1 61 61 ALA N N 15 122.278 0.05 . 1 . . . . . . . . 5908 1 124 . 1 1 62 62 GLU H H 1 8.237 0.01 . 1 . . . . . . . . 5908 1 125 . 1 1 62 62 GLU N N 15 116.639 0.05 . 1 . . . . . . . . 5908 1 126 . 1 1 63 63 ARG H H 1 7.804 0.01 . 1 . . . . . . . . 5908 1 127 . 1 1 63 63 ARG N N 15 119.045 0.05 . 1 . . . . . . . . 5908 1 128 . 1 1 64 64 GLU H H 1 7.904 0.01 . 1 . . . . . . . . 5908 1 129 . 1 1 64 64 GLU N N 15 119.274 0.05 . 1 . . . . . . . . 5908 1 130 . 1 1 65 65 LYS H H 1 8.014 0.01 . 1 . . . . . . . . 5908 1 131 . 1 1 65 65 LYS N N 15 121.726 0.05 . 1 . . . . . . . . 5908 1 132 . 1 1 66 66 LYS H H 1 7.983 0.01 . 1 . . . . . . . . 5908 1 133 . 1 1 66 66 LYS N N 15 127.350 0.05 . 1 . . . . . . . . 5908 1 stop_ save_