data_5839 ####################### # Entry information # ####################### save_entry_information _Saveframe_category entry_information _Entry_title ; Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G ; _BMRB_accession_number 5839 _BMRB_flat_file_name bmr5839.str _Entry_type original _Submission_date 2003-06-22 _Accession_date 2003-06-23 _Entry_origination author _NMR_STAR_version 2.1.1 _Experimental_method NMR _Details . loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hall Jennifer B. . 2 Fushman David . . stop_ loop_ _Saveframe_category_type _Saveframe_category_type_count T1_relaxation 1 T2_relaxation 1 heteronucl_NOE 1 stop_ loop_ _Data_type _Data_type_count "T1 relaxation values" 51 "T2 relaxation values" 51 stop_ loop_ _Revision_date _Revision_keyword _Revision_author _Revision_detail 2007-06-11 update author 'add related entry' 2002-01-01 original author 'original release' stop_ loop_ _Related_BMRB_accession_number _Relationship 15283 'Solid-State C and N Chemical Shifts of GB3' stop_ save_ ############################# # Citation for this entry # ############################# save_entry_citation _Saveframe_category entry_citation _Citation_full . _Citation_title ; Characterization of the Overall and Local Dynamics of a Protein with Intermediate Rotational Anisotropy: Differentiating Between Conformational Exchange and Anisotropic Diffusion in the B3 Domain of Protein G ; _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code 22855801 _PubMed_ID 12975584 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Hall Jennifer B. . 2 Fushman David . . stop_ _Journal_abbreviation 'J. Biomol. NMR' _Journal_volume 27 _Journal_issue 3 _Journal_CSD . _Book_chapter_title . _Book_volume . _Book_series . _Book_ISBN . _Conference_state_province . _Conference_abstract_number . _Page_first 261 _Page_last 275 _Year 2003 _Details . save_ ####################################### # Cited references within the entry # ####################################### save_ref_1 _Saveframe_category citation _Citation_full ; Fushman, D., Cahill, S. and Cowburn, D. (1997) J. Mol. Biol., 266, 173-194. ; _Citation_title 'The main-chain dynamics of the dynamin pleckstrin homology (PH) domain in solution: analysis of 15N relaxation with monomer/dimer equilibration.' _Citation_status published _Citation_type journal _CAS_abstract_code . _MEDLINE_UI_code . _PubMed_ID 9054979 loop_ _Author_ordinal _Author_family_name _Author_given_name _Author_middle_initials _Author_family_title 1 Fushman D. . . 2 Cahill S. . . 3 Cowburn D. . . stop_ _Journal_abbreviation 'J. Mol. Biol.' _Journal_name_full 'Journal of molecular biology' _Journal_volume 266 _Journal_issue 1 _Journal_CSD . _Book_title . _Book_chapter_title . _Book_volume . _Book_series . _Book_publisher . _Book_publisher_city . _Book_ISBN . _Conference_title . _Conference_site . _Conference_state_province . _Conference_country . _Conference_start_date . _Conference_end_date . _Conference_abstract_number . _Thesis_institution . _Thesis_institution_city . _Thesis_institution_country . _Page_first 173 _Page_last 194 _Year 1997 _Details ; The backbone dynamics of the pleckstrin homology (PH) domain from dynamin were studied by 15N NMR relaxation (R1 and R2) and steady state heteronuclear 15N [1H] nuclear Overhauser effect measurements at 500 and 600 MHz, at protein concentrations of 1.7 mM and 300 microM, and by molecular dynamics (MD) simulations. The analysis was performed using the model-free approach. The method was extended in order to account for observed partial (equilibrium) dimerization of the protein at NMR concentrations. A model is developed that takes into account both rapid monomer-dimer exchange and anisotropy of the over-all rotation of the dimer. The data show complex dynamics of the dynamin PH domain. Internal motions in elements of the secondary structure are restricted, as inferred from the high value of the order parameter (S2 approximately 0.9) and from the local correlation time < 100 ps. Of the four extended loop regions that are disordered in the NMR-derived solution structure of the protein, loops beta 1/beta 2 and beta 5/beta 6 are involved in a large-amplitude (S2 down to 0.2 to 0.3) subnanosecond to nanosecond time-scale motion. Reorientation of the loops beta 3/beta 4 and beta 6/beta 7, in contrast, is restricted, characterized by the values of order parameter S2 approximately 0.9 more typical of the protein core. These loops, however, are involved in much slower processes of motion resulting in a conformational exchange on a microsecond to submillisecond time scale. The motions of the terminal regions (residues 1 to 10, 122 to 125) are practically unrestricted (S2 down to 0.05, characteristic times in nanosecond time scale), suggesting that these parts of the sequence do not participate in the protein fold. The analysis shows a larger sensitivity of the 15N relaxation data to protein microdynamic parameters (S2, tau loc) when protein molecular mass (tau c) increases. The use of negative values of the steady state 15N[1H] NOEs as an indicator of the residues not belonging to the folded structure is suggested. The amplitudes of local motion observed in the MD simulation are in a good-agreement with the NMR data for the amide NH groups located in the protein core. ; save_ ################################## # Molecular system description # ################################## save_system_GB3 _Saveframe_category molecular_system _Mol_system_name GB3 _Abbreviation_common GB3 _Enzyme_commission_number . loop_ _Mol_system_component_name _Mol_label 'GB3 subunit 1' $GB3 stop_ _System_molecular_weight . _System_physical_state native _System_oligomer_state monomer _System_paramagnetic no _System_thiol_state 'not present' _Database_query_date . _Details . save_ ######################## # Monomeric polymers # ######################## save_GB3 _Saveframe_category monomeric_polymer _Mol_type polymer _Mol_polymer_class protein _Name_common 'B3 domain of Streptococcal protein G' _Abbreviation_common GB3 _Molecular_mass . _Mol_thiol_state 'not present' _Details . ############################## # Polymer residue sequence # ############################## _Residue_count 56 _Mol_residue_sequence ; MQYKLVINGKTLKGETTTKA VDAETAEKAFKQYANDNGVD GVWTYDDATKTFTVTE ; loop_ _Residue_seq_code _Residue_label 1 MET 2 GLN 3 TYR 4 LYS 5 LEU 6 VAL 7 ILE 8 ASN 9 GLY 10 LYS 11 THR 12 LEU 13 LYS 14 GLY 15 GLU 16 THR 17 THR 18 THR 19 LYS 20 ALA 21 VAL 22 ASP 23 ALA 24 GLU 25 THR 26 ALA 27 GLU 28 LYS 29 ALA 30 PHE 31 LYS 32 GLN 33 TYR 34 ALA 35 ASN 36 ASP 37 ASN 38 GLY 39 VAL 40 ASP 41 GLY 42 VAL 43 TRP 44 THR 45 TYR 46 ASP 47 ASP 48 ALA 49 THR 50 LYS 51 THR 52 PHE 53 THR 54 VAL 55 THR 56 GLU stop_ _Sequence_homology_query_date . _Sequence_homology_query_revised_last_date 2015-01-28 loop_ _Database_name _Database_accession_code _Database_entry_mol_name _Sequence_query_to_submitted_percentage _Sequence_subject_length _Sequence_identity _Sequence_positive _Sequence_homology_expectation_value BMRB 15283 GB3 100.00 56 100.00 100.00 4.05e-30 BMRB 18531 GB3 100.00 56 100.00 100.00 4.05e-30 BMRB 2575 "IgG Fc region-binding protein" 100.00 56 98.21 98.21 4.80e-29 PDB 1IGC "Igg1 Fab Fragment (Mopc21) Complex With Domain Iii Of Protein G From Streptococcus" 96.43 61 100.00 100.00 2.16e-28 PDB 1IGD "The Third Igg-Binding Domain From Streptococcal Protein G: An Analysis By X-Ray Crystallography Of The Structure Alone And In A" 96.43 61 100.00 100.00 2.16e-28 PDB 1P7E "Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings" 100.00 56 100.00 100.00 4.05e-30 PDB 1P7F "Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings" 100.00 56 100.00 100.00 4.05e-30 PDB 1PGX "The 1.66 Angstroms X-Ray Structure Of The B2 Immunoglobulin- Binding Domain Of Streptococcal Protein G And Comparison To The Nm" 96.43 83 100.00 100.00 1.08e-28 PDB 2IGD "Anisotropic Structure Of Protein G Igg-Binding Domain Iii At 1.1 Angstrom Resolution" 96.43 61 100.00 100.00 2.16e-28 PDB 2IGH "Determination Of The Solution Structures Of Domains Ii And Iii Of Protein G From Streptococcus By 1h Nmr" 96.43 61 100.00 100.00 2.33e-28 PDB 2LUM "Three-State Ensemble Obtained From Enoes Of The Third Immunoglobulin Binding Domain Of Protein G (Gb3)" 100.00 56 100.00 100.00 4.05e-30 PDB 2NMQ "Simultaneous Determination Of Protein Structure And Dynamics Using Rdcs" 96.43 55 100.00 100.00 3.57e-28 PDB 2OED "Gb3 Solution Structure Obtained By Refinement Of X-Ray Structure With Dipolar Couplings" 100.00 56 100.00 100.00 4.05e-30 GB AAA26921 "mag [Streptococcus dysgalactiae]" 96.43 413 98.15 100.00 7.02e-27 GB AAB27024 "protein G IgG Fc binding domain [Streptococcus sp. CMCC 32138]" 96.43 60 98.15 98.15 1.38e-27 GB ABL60854 "NTAP(GS) [Expression vector pCeMM-NTAP(GS)-Gw]" 96.43 176 100.00 100.00 3.39e-27 GB ABL60859 "CTAP(SG) [Expression vector pCeMM-CTAP(SG)-Gw]" 96.43 190 100.00 100.00 4.28e-27 GB ABO76907 "NTAP(GS) [Expression vector pCeMM-NTAP(GS)]" 96.43 176 100.00 100.00 3.39e-27 stop_ save_ #################### # Natural source # #################### save_natural_source _Saveframe_category natural_source loop_ _Mol_label _Organism_name_common _NCBI_taxonomy_ID _Superkingdom _Kingdom _Genus _Species $GB3 . 1301 Eubacteria . Streptococcus . stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Saveframe_category experimental_source loop_ _Mol_label _Production_method _Host_organism_name_common _Genus _Species _Strain _Vector_name $GB3 'recombinant technology' . . . . . stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_one _Saveframe_category sample _Sample_type solution _Details . loop_ _Mol_label _Concentration_value _Concentration_value_units _Isotopic_labeling $GB3 1.8 mM [U-15N] stop_ save_ ############################ # Computer software used # ############################ save_XWINNMR _Saveframe_category software _Name XWINNMR _Version 3.0 loop_ _Task 'NMR data processing' stop_ _Details 'Bruker Instruments' save_ save_RELAXFIT _Saveframe_category software _Name RELAXFIT _Version . loop_ _Task 'curve fitting' 'error estimation' stop_ _Details ; In-house developed software for fitting relaxation data to relaxation curve. Fushman, D., Cahill, S. and Cowburn, D. (1997) J. Mol. Biol., 266, 173-194. ; save_ save_AUTOPICK _Saveframe_category software _Name AUTOPICK _Version . loop_ _Task 'peak picking' 'intensity calculation' stop_ _Details ; In-house developed software for automatic peak picking, lineshape fitting, and peak integration. Fushman, D., Cahill, S. and Cowburn, D. (1997) J. Mol. Biol., 266, 173-194. ; save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer _Saveframe_category NMR_spectrometer _Manufacturer Bruker _Model DRX _Field_strength 600 _Details . save_ ############################# # NMR applied experiments # ############################# save_15N_R1_1 _Saveframe_category NMR_applied_experiment _Experiment_name '15N R1' _Sample_label $sample_one save_ save_15N_R2_2 _Saveframe_category NMR_applied_experiment _Experiment_name '15N R2' _Sample_label $sample_one save_ save_15N-1H_NOE_3 _Saveframe_category NMR_applied_experiment _Experiment_name '15N-1H NOE' _Sample_label $sample_one save_ save_NMR_spec_expt__0_1 _Saveframe_category NMR_applied_experiment _Experiment_name '15N R1' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_2 _Saveframe_category NMR_applied_experiment _Experiment_name '15N R2' _BMRB_pulse_sequence_accession_number . _Details . save_ save_NMR_spec_expt__0_3 _Saveframe_category NMR_applied_experiment _Experiment_name '15N-1H NOE' _BMRB_pulse_sequence_accession_number . _Details . save_ ####################### # Sample conditions # ####################### save_sample_conditions_one _Saveframe_category sample_conditions _Details . loop_ _Variable_type _Variable_value _Variable_value_error _Variable_value_units pH 5.8 0.2 n/a temperature 297 1 K stop_ save_ save_15N_T1_set_1 _Saveframe_category T1_relaxation _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Spectrometer_frequency_1H 600 _T1_coherence_type Nz _T1_value_units s _Mol_system_component_name 'GB3 subunit 1' _Text_data_format . _Text_data . loop_ _T1_ID _Residue_seq_code _Residue_label _Atom_name _T1_value _T1_value_error 1 2 GLN N 0.441 0.0015 2 3 TYR N 0.439 0.0006 3 4 LYS N 0.424 0.0000 4 5 LEU N 0.417 0.0017 5 6 VAL N 0.422 0.0013 6 7 ILE N 0.427 0.0009 7 8 ASN N 0.429 0.0006 8 9 GLY N 0.437 0.0012 9 10 LYS N 0.448 0.0004 10 11 THR N 0.472 0.0006 11 12 LEU N 0.535 0.0009 12 13 LYS N 0.469 0.0005 13 14 GLY N 0.490 0.0011 14 16 THR N 0.439 0.0006 15 17 THR N 0.455 0.0003 16 18 THR N 0.433 0.0008 17 19 LYS N 0.469 0.0005 18 20 ALA N 0.448 0.0003 19 21 VAL N 0.435 0.0003 20 22 ASP N 0.427 0.0003 21 23 ALA N 0.433 0.0012 22 24 GLU N 0.450 0.0007 23 26 ALA N 0.412 0.0007 24 28 LYS N 0.427 0.0006 25 29 ALA N 0.422 0.0006 26 30 PHE N 0.424 0.0007 27 31 LYS N 0.422 0.0007 28 32 GLN N 0.431 0.0011 29 33 TYR N 0.422 0.0009 30 34 ALA N 0.415 0.0004 31 36 ASP N 0.429 0.0007 32 37 ASN N 0.448 0.0007 33 38 GLY N 0.437 0.0017 34 39 VAL N 0.442 0.0005 35 40 ASP N 0.500 0.0008 36 41 GLY N 0.592 0.0024 37 42 VAL N 0.437 0.0005 38 43 TRP N 0.427 0.0007 39 44 THR N 0.426 0.0009 40 45 TYR N 0.448 0.0008 41 46 ASP N 0.429 0.0009 42 47 ASP N 0.448 0.0008 43 48 ALA N 0.472 0.0005 44 49 THR N 0.450 0.0012 45 50 LYS N 0.415 0.0004 46 51 THR N 0.426 0.0014 47 52 PHE N 0.422 0.0010 48 53 THR N 0.435 0.0012 49 54 VAL N 0.410 0.0012 50 55 THR N 0.424 0.0017 51 56 GLU N 0.427 0.0011 stop_ save_ save_15N_T2_set_1 _Saveframe_category T2_relaxation _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Spectrometer_frequency_1H 600 _T2_coherence_type Ny _T2_value_units s _Mol_system_component_name 'GB3 subunit 1' _Text_data_format . _Text_data . loop_ _T2_ID _Residue_seq_code _Residue_label _Atom_name _T2_value _T2_value_error _Rex_value _Rex_error 1 2 GLN N 0.198 0.0034 . . 2 3 TYR N 0.207 0.0011 . . 3 4 LYS N 0.196 0.0015 . . 4 5 LEU N 0.198 0.0025 . . 5 6 VAL N 0.198 0.0044 . . 6 7 ILE N 0.204 0.0008 . . 7 8 ASN N 0.197 0.0017 . . 8 9 GLY N 0.204 0.0021 . . 9 10 LYS N 0.211 0.0009 . . 10 11 THR N 0.217 0.0019 . . 11 12 LEU N 0.265 0.0026 . . 12 13 LYS N 0.213 0.0012 . . 13 14 GLY N 0.233 0.0038 . . 14 16 THR N 0.206 0.0020 . . 15 17 THR N 0.211 0.0026 . . 16 18 THR N 0.201 0.0013 . . 17 19 LYS N 0.221 0.0010 . . 18 20 ALA N 0.217 0.0008 . . 19 21 VAL N 0.203 0.0016 . . 20 22 ASP N 0.190 0.0027 . . 21 23 ALA N 0.187 0.0021 . . 22 24 GLU N 0.188 0.0008 . . 23 26 ALA N 0.185 0.0015 . . 24 28 LYS N 0.175 0.0017 . . 25 29 ALA N 0.180 0.0013 . . 26 30 PHE N 0.180 0.0016 . . 27 31 LYS N 0.170 0.0008 . . 28 32 GLN N 0.175 0.0020 . . 29 33 TYR N 0.179 0.0015 . . 30 34 ALA N 0.175 0.0005 . . 31 36 ASP N 0.175 0.0007 . . 32 37 ASN N 0.197 0.0019 . . 33 38 GLY N 0.195 0.0004 . . 34 39 VAL N 0.174 0.0020 . . 35 40 ASP N 0.213 0.0029 . . 36 41 GLY N 0.281 0.0029 . . 37 42 VAL N 0.198 0.0010 . . 38 43 TRP N 0.193 0.0041 . . 39 44 THR N 0.197 0.0006 . . 40 45 TYR N 0.210 0.0017 . . 41 46 ASP N 0.207 0.0022 . . 42 47 ASP N 0.214 0.0016 . . 43 48 ALA N 0.211 0.0013 . . 44 49 THR N 0.206 0.0014 . . 45 50 LYS N 0.197 0.0014 . . 46 51 THR N 0.203 0.0012 . . 47 52 PHE N 0.192 0.0028 . . 48 53 THR N 0.202 0.0014 . . 49 54 VAL N 0.192 0.0005 . . 50 55 THR N 0.200 0.0012 . . 51 56 GLU N 0.193 0.0019 . . stop_ save_ save_heteronuclear_NOE_set_1 _Saveframe_category heteronuclear_NOE _Details . loop_ _Sample_label $sample_one stop_ _Sample_conditions_label $sample_conditions_one _Spectrometer_frequency_1H 600 _Mol_system_component_name 'GB3 subunit 1' _Atom_one_atom_name N _Atom_two_atom_name H _Heteronuclear_NOE_value_type . _NOE_reference_value . _NOE_reference_description . _Text_data_format . _Text_data . loop_ _Residue_seq_code _Residue_label _Heteronuclear_NOE_value _Heteronuclear_NOE_value_error 2 GLN 0.646 0.004 3 TYR 0.706 0.004 4 LYS 0.700 0.004 5 LEU 0.713 0.004 6 VAL 0.714 0.004 7 ILE 0.699 0.004 8 ASN 0.699 0.004 9 GLY 0.684 0.004 10 LYS 0.647 0.003 11 THR 0.608 0.004 12 LEU 0.597 0.003 13 LYS 0.627 0.004 14 GLY 0.656 0.003 16 THR 0.699 0.003 17 THR 0.680 0.004 18 THR 0.708 0.003 19 LYS 0.687 0.004 20 ALA 0.680 0.003 21 VAL 0.688 0.003 22 ASP 0.702 0.003 23 ALA 0.757 0.003 24 GLU 0.741 0.003 26 ALA 0.750 0.003 28 LYS 0.734 0.003 29 ALA 0.741 0.003 30 PHE 0.740 0.003 31 LYS 0.747 0.003 32 GLN 0.742 0.003 33 TYR 0.742 0.003 34 ALA 0.754 0.003 36 ASP 0.762 0.003 37 ASN 0.733 0.004 38 GLY 0.722 0.003 39 VAL 0.720 0.004 40 ASP 0.591 0.003 41 GLY 0.422 0.002 42 VAL 0.723 0.004 43 TRP 0.704 0.004 44 THR 0.710 0.004 45 TYR 0.730 0.004 46 ASP 0.714 0.004 47 ASP 0.703 0.003 48 ALA 0.708 0.003 49 THR 0.738 0.004 50 LYS 0.715 0.003 51 THR 0.719 0.004 52 PHE 0.727 0.005 53 THR 0.704 0.004 54 VAL 0.705 0.004 55 THR 0.708 0.004 56 GLU 0.681 0.004 stop_ save_