data_34162 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID 34162 _Entry.Title ; Structure of minimal i-motif domain ; _Entry.Type macromolecule _Entry.Version_type original _Entry.Submission_date 2017-07-12 _Entry.Accession_date 2017-11-22 _Entry.Last_release_date 2017-11-22 _Entry.Original_release_date 2017-11-22 _Entry.Origination author _Entry.Format_name . _Entry.NMR_STAR_version 3.2.0.16 _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype SOLUTION _Entry.Source_data_format . _Entry.Source_data_format_version . _Entry.Generated_software_name . _Entry.Generated_software_version . _Entry.Generated_software_ID . _Entry.Generated_software_label . _Entry.Generated_date . _Entry.DOI . _Entry.UUID . _Entry.Related_coordinate_file_name . _Entry.Details . 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.ORCID _Entry_author.Entry_ID 1 B. Mir B. . . . 34162 2 I. Serrano I. . . . 34162 3 D. Buitrago D. . . . 34162 4 M. Orozco M. . . . 34162 5 N. Escaja N. . . . 34162 6 C. Gonzalez C. . . . 34162 stop_ loop_ _Struct_keywords.Keywords _Struct_keywords.Text _Struct_keywords.Entry_ID DNA . 34162 'DNA non-canonical structure' . 34162 i-motif . 34162 'minor groove tetrad' . 34162 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 34162 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '1H chemical shifts' 116 34162 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 . . 2017-11-27 . original BMRB . 34162 stop_ loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID PDB 5OGA 'BMRB Entry Tracking System' 34162 stop_ save_ ############### # Citations # ############### save_citation_1 _Citation.Sf_category citations _Citation.Sf_framecode citation_1 _Citation.Entry_ID 34162 _Citation.ID 1 _Citation.Class 'entry citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.DOI . _Citation.PubMed_ID 28933543 _Citation.Full_citation . _Citation.Title ; Prevalent Sequences in the Human Genome Can Form Mini i-Motif Structures at Physiological pH. ; _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev 'J. Am. Chem. Soc.' _Citation.Journal_name_full . _Citation.Journal_volume 139 _Citation.Journal_issue . _Citation.Journal_ASTM JACSAT _Citation.Journal_ISSN 1520-5126 _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 13985 _Citation.Page_last 13988 _Citation.Year 2017 _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.ORCID _Citation_author.Entry_ID _Citation_author.Citation_ID 1 B. Mir B. . . . 34162 1 2 I. Serrano I. . . . 34162 1 3 D. Buitrago D. . . . 34162 1 4 M. Orozco M. . . . 34162 1 5 N. Escaja N. . . . 34162 1 6 C. Gonzalez C. . . . 34162 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID 34162 _Assembly.ID 1 _Assembly.Name ; DNA (5'-D(*TP*(DCP)P*GP*TP*TP*CP*(DCP)P*GP*TP*TP*TP*TP*TP*CP*GP*TP*TP*CP*CP*GP*T)-3') ; _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 . _Assembly.Molecular_mass . _Assembly.Enzyme_commission_number . _Assembly.Details . _Assembly.DB_query_date . _Assembly.DB_query_revised_last_date . 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 entity_1 1 $entity_1 A A yes . . . . . . 34162 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID 34162 _Entity.ID 1 _Entity.BMRB_code . _Entity.Name entity_1 _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_type_details . _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code_can . _Entity.Polymer_seq_one_letter_code ; XCGTTCCGTTTTTCGTTCCG T ; _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 yes _Entity.Nstd_chirality . _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 21 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Src_method syn _Entity.Parent_entity_ID 1 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight 6275.114 _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details . _Entity.DB_query_date . _Entity.DB_query_revised_last_date . 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 . THM . 34162 1 2 . DNR . 34162 1 3 . DG . 34162 1 4 . DT . 34162 1 5 . DT . 34162 1 6 . DC . 34162 1 7 . DNR . 34162 1 8 . DG . 34162 1 9 . DT . 34162 1 10 . DT . 34162 1 11 . DT . 34162 1 12 . DT . 34162 1 13 . DT . 34162 1 14 . DC . 34162 1 15 . DG . 34162 1 16 . DT . 34162 1 17 . DT . 34162 1 18 . DC . 34162 1 19 . DC . 34162 1 20 . DG . 34162 1 21 . DT . 34162 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 . THM 1 1 34162 1 . DNR 2 2 34162 1 . DG 3 3 34162 1 . DT 4 4 34162 1 . DT 5 5 34162 1 . DC 6 6 34162 1 . DNR 7 7 34162 1 . DG 8 8 34162 1 . DT 9 9 34162 1 . DT 10 10 34162 1 . DT 11 11 34162 1 . DT 12 12 34162 1 . DT 13 13 34162 1 . DC 14 14 34162 1 . DG 15 15 34162 1 . DT 16 16 34162 1 . DT 17 17 34162 1 . DC 18 18 34162 1 . DC 19 19 34162 1 . DG 20 20 34162 1 . DT 21 21 34162 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 34162 _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.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.Secretion _Entity_natural_src.Plasmid _Entity_natural_src.Gene_mnemonic _Entity_natural_src.Details _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $entity_1 . . 'no natural source' . . . . . . . . . . . . . . . . . . . . . . 34162 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 34162 _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_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.Details _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $entity_1 . 'chemical synthesis' . . . . . . . . . . . . . . . . 34162 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_DNR _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_DNR _Chem_comp.Entry_ID 34162 _Chem_comp.ID DNR _Chem_comp.Provenance PDB _Chem_comp.Name "2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE" _Chem_comp.Type 'DNA LINKING' _Chem_comp.BMRB_code DNR _Chem_comp.PDB_code DNR _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2012-11-20 _Chem_comp.Modified_date 2012-11-20 _Chem_comp.Release_status REL _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code C _Chem_comp.Three_letter_code DNR _Chem_comp.Number_atoms_all 35 _Chem_comp.Number_atoms_nh 20 _Chem_comp.Atom_nomenclature_source . _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code ; InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/p+1/t5-,6+,8+/m0/s1 ; _Chem_comp.Mon_nstd_flag . _Chem_comp.Mon_nstd_class . _Chem_comp.Mon_nstd_details . _Chem_comp.Mon_nstd_parent . _Chem_comp.Mon_nstd_parent_comp_ID DC _Chem_comp.Std_deriv_one_letter_code . _Chem_comp.Std_deriv_three_letter_code . _Chem_comp.Std_deriv_BMRB_code . _Chem_comp.Std_deriv_PDB_code . _Chem_comp.Std_deriv_chem_comp_name . _Chem_comp.Synonyms . _Chem_comp.Formal_charge 1 _Chem_comp.Paramagnetic . _Chem_comp.Aromatic no _Chem_comp.Formula 'C9 H15 N3 O7 P' _Chem_comp.Formula_weight 308.205 _Chem_comp.Formula_mono_iso_wt_nat . _Chem_comp.Formula_mono_iso_wt_13C . _Chem_comp.Formula_mono_iso_wt_15N . _Chem_comp.Formula_mono_iso_wt_13C_15N . _Chem_comp.Image_file_name . _Chem_comp.Image_file_format . _Chem_comp.Topo_file_name . _Chem_comp.Topo_file_format . _Chem_comp.Struct_file_name . _Chem_comp.Struct_file_format . _Chem_comp.Stereochem_param_file_name . _Chem_comp.Stereochem_param_file_format . _Chem_comp.Model_details . _Chem_comp.Model_erf . _Chem_comp.Model_source . _Chem_comp.Model_coordinates_details . _Chem_comp.Model_coordinates_missing_flag yes _Chem_comp.Ideal_coordinates_details . _Chem_comp.Ideal_coordinates_missing_flag no _Chem_comp.Model_coordinates_db_code 1LAQ _Chem_comp.Processing_site RCSB _Chem_comp.Vendor . _Chem_comp.Vendor_product_code . _Chem_comp.Details . _Chem_comp.DB_query_date . _Chem_comp.DB_last_query_revised_last_date . loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID C1C(C(OC1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O SMILES 'OpenEye OEToolkits' 1.5.0 34162 DNR C1[C@@H]([C@H](O[C@H]1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 34162 DNR ; InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/p+1/t5-,6+,8+/m0/s1 ; InChI InChI 1.03 34162 DNR NC1=[NH+]C(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2 SMILES_CANONICAL CACTVS 3.341 34162 DNR NC1=[NH+]C(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2 SMILES CACTVS 3.341 34162 DNR NCMVOABPESMRCP-SHYZEUOFSA-O InChIKey InChI 1.03 34162 DNR O=C1[NH+]=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O SMILES ACDLabs 10.04 34162 DNR stop_ loop_ _Chem_comp_identifier.Identifier _Chem_comp_identifier.Type _Chem_comp_identifier.Program _Chem_comp_identifier.Program_version _Chem_comp_identifier.Entry_ID _Chem_comp_identifier.Comp_ID "2'-deoxy-5'-cytidylic acid" 'SYSTEMATIC NAME' ACDLabs 10.04 34162 DNR ; [(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate ; 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 34162 DNR stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.BMRB_code _Chem_comp_atom.PDB_atom_ID _Chem_comp_atom.Alt_atom_ID _Chem_comp_atom.Auth_atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Isotope_number _Chem_comp_atom.Chirality _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Partial_charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Align _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.Leaving_atom_flag _Chem_comp_atom.Substruct_code _Chem_comp_atom.Ionizable _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_x_esd _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_y_esd _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.Model_Cartn_z_esd _Chem_comp_atom.Model_Cartn_x_ideal _Chem_comp_atom.Model_Cartn_y_ideal _Chem_comp_atom.Model_Cartn_z_ideal _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Details _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID P P P P . P . . N 0 . . . 1 no no . . . . -0.684 . -7.446 . 15.813 . -3.968 -1.665 3.118 1 . 34162 DNR OP1 OP1 OP1 O1P . O . . N 0 . . . 1 no no . . . . 0.421 . -7.036 . 14.917 . -4.406 -2.599 4.208 2 . 34162 DNR OP2 OP2 OP2 O2P . O . . N 0 . . . 1 no no . . . . -1.407 . -8.711 . 15.556 . -3.912 -2.311 1.636 3 . 34162 DNR O5' O5' O5' O5* . O . . N 0 . . . 1 no no . . . . -1.767 . -6.248 . 15.855 . -2.493 -1.028 3.315 4 . 34162 DNR C5' C5' C5' C5* . C . . N 0 . . . 1 no no . . . . -2.936 . -6.352 . 16.678 . -2.005 -0.136 2.327 5 . 34162 DNR C4' C4' C4' C4* . C . . R 0 . . . 1 no no . . . . -3.852 . -5.142 . 16.542 . -0.611 0.328 2.728 6 . 34162 DNR O4' O4' O4' O4* . O . . N 0 . . . 1 no no . . . . -3.125 . -3.913 . 16.795 . 0.247 -0.829 2.764 7 . 34162 DNR C1' C1' C1' C1* . C . . R 0 . . . 1 no no . . . . -3.181 . -3.066 . 15.625 . 1.157 -0.778 1.657 8 . 34162 DNR N1 N1 N1 N1 . N . . N 0 . . . 1 no no . . . . -1.853 . -2.469 . 15.339 . 1.164 -2.047 0.989 9 . 34162 DNR C6 C6 C6 C6 . C . . N 0 . . . 1 no no . . . . -0.754 . -3.262 . 15.217 . -0.015 -2.783 0.959 10 . 34162 DNR C2 C2 C2 C2 . C . . N 0 . . . 1 no no . . . . -1.760 . -1.079 . 15.249 . 2.335 -2.532 0.381 11 . 34162 DNR O2 O2 O2 O2 . O . . N 0 . . . 1 no no . . . . -2.767 . -0.382 . 15.363 . 3.425 -1.977 0.342 12 . 34162 DNR N3 N3 N3 N3 . N . . N 1 . . . 1 no no . . . . -0.527 . -0.524 . 15.041 . 2.203 -3.824 -0.257 13 . 34162 DNR C4 C4 C4 C4 . C . . N 0 . . . 1 no no . . . . 0.561 . -1.305 . 14.927 . 1.089 -4.548 -0.301 14 . 34162 DNR N4 N4 N4 N4 . N . . N 0 . . . 1 no no . . . . 1.753 . -0.747 . 14.733 . 0.968 -5.729 -0.886 15 . 34162 DNR C5 C5 C5 C5 . C . . N 0 . . . 1 no no . . . . 0.463 . -2.728 . 15.014 . -0.107 -3.974 0.362 16 . 34162 DNR C2' C2' C2' C2* . C . . N 0 . . . 1 no no . . . . -3.671 . -3.939 . 14.490 . 0.710 0.360 0.754 17 . 34162 DNR C3' C3' C3' C3* . C . . S 0 . . . 1 no no . . . . -4.447 . -5.040 . 15.147 . 0.008 1.286 1.720 18 . 34162 DNR O3' O3' O3' O3* . O . . N 0 . . . 1 no no . . . . -5.846 . -4.728 . 15.206 . 0.965 2.121 2.368 19 . 34162 DNR OP3 OP3 OP3 O3P . O . . N 0 . . . 1 no yes . . . . . . . . . . -4.901 -0.360 2.920 20 . 34162 DNR HOP2 HOP2 HOP2 2HOP . H . . N 0 . . . 0 no no . . . . -2.116 . -8.974 . 16.130 . -4.684 -2.823 1.313 21 . 34162 DNR H5' H5' H5' 1H5* . H . . N 0 . . . 1 no no . . . . -2.630 . -6.429 . 17.716 . -1.971 -0.654 1.366 22 . 34162 DNR H5'' H5'' H5'' 2H5* . H . . N 0 . . . 0 no no . . . . -3.489 . -7.251 . 16.403 . -2.683 0.718 2.254 23 . 34162 DNR H4' H4' H4' H4* . H . . N 0 . . . 1 no no . . . . -4.660 . -5.225 . 17.266 . -0.644 0.753 3.736 24 . 34162 DNR H1' H1' H1' H1* . H . . N 0 . . . 1 no no . . . . -3.901 . -2.280 . 15.793 . 2.163 -0.604 2.054 25 . 34162 DNR H6 H6 H6 H6 . H . . N 0 . . . 1 no no . . . . -0.864 . -4.341 . 15.274 . -0.871 -2.335 1.453 26 . 34162 DNR HN3 HN3 HN3 HN3 . H . . N 0 . . . 1 no no . . . . -0.421 . 0.491 . 15.056 . 3.017 -4.226 -0.715 27 . 34162 DNR H41 H41 H41 H41 . H . . N 0 . . . 1 no no . . . . 1.833 . 0.257 . 14.671 . 0.511 -5.815 -1.789 28 . 34162 DNR H42 H42 H42 H42 . H . . N 0 . . . 1 no no . . . . 2.576 . -1.326 . 14.649 . 1.332 -6.567 -0.439 29 . 34162 DNR H5 H5 H5 H5 . H . . N 0 . . . 1 no no . . . . 1.346 . -3.360 . 14.919 . -1.040 -4.526 0.354 30 . 34162 DNR H2' H2' H2' 1H2* . H . . N 0 . . . 1 no no . . . . -2.839 . -4.348 . 13.921 . -0.003 -0.001 0.003 31 . 34162 DNR H2'' H2'' H2'' 2H2* . H . . N 0 . . . 0 no no . . . . -4.322 . -3.365 . 13.847 . 1.556 0.818 0.232 32 . 34162 DNR H3' H3' H3' H3* . H . . N 0 . . . 1 no no . . . . -4.291 . -5.978 . 14.608 . -0.722 1.941 1.236 33 . 34162 DNR HO3' HO3' HO3' H3T . H . . N 0 . . . 0 no yes . . . . -6.217 . -4.664 . 14.334 . 0.743 3.042 2.146 34 . 34162 DNR HOP3 HOP3 HOP3 3HOP . H . . N 0 . . . 0 no no . . . . -0.709 . -0.263 . 0.574 . -5.874 -0.475 2.871 35 . 34162 DNR stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 . DOUB P OP1 no N 1 . 34162 DNR 2 . SING P OP2 no N 2 . 34162 DNR 3 . SING P O5' no N 3 . 34162 DNR 4 . SING P OP3 no N 4 . 34162 DNR 5 . SING OP2 HOP2 no N 5 . 34162 DNR 6 . SING O5' C5' no N 6 . 34162 DNR 7 . SING C5' C4' no N 7 . 34162 DNR 8 . SING C5' H5' no N 8 . 34162 DNR 9 . SING C5' H5'' no N 9 . 34162 DNR 10 . SING C4' O4' no N 10 . 34162 DNR 11 . SING C4' C3' no N 11 . 34162 DNR 12 . SING C4' H4' no N 12 . 34162 DNR 13 . SING O4' C1' no N 13 . 34162 DNR 14 . SING C1' N1 no N 14 . 34162 DNR 15 . SING C1' C2' no N 15 . 34162 DNR 16 . SING C1' H1' no N 16 . 34162 DNR 17 . SING N1 C6 no N 17 . 34162 DNR 18 . SING N1 C2 no N 18 . 34162 DNR 19 . DOUB C6 C5 no N 19 . 34162 DNR 20 . SING C6 H6 no N 20 . 34162 DNR 21 . DOUB C2 O2 no N 21 . 34162 DNR 22 . SING C2 N3 no N 22 . 34162 DNR 23 . DOUB N3 C4 no N 23 . 34162 DNR 24 . SING N3 HN3 no N 24 . 34162 DNR 25 . SING C4 N4 no N 25 . 34162 DNR 26 . SING C4 C5 no N 26 . 34162 DNR 27 . SING N4 H41 no N 27 . 34162 DNR 28 . SING N4 H42 no N 28 . 34162 DNR 29 . SING C5 H5 no N 29 . 34162 DNR 30 . SING C2' C3' no N 30 . 34162 DNR 31 . SING C2' H2' no N 31 . 34162 DNR 32 . SING C2' H2'' no N 32 . 34162 DNR 33 . SING C3' O3' no N 33 . 34162 DNR 34 . SING C3' H3' no N 34 . 34162 DNR 35 . SING O3' HO3' no N 35 . 34162 DNR 36 . SING OP3 HOP3 no N 36 . 34162 DNR stop_ save_ save_chem_comp_THM _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_THM _Chem_comp.Entry_ID 34162 _Chem_comp.ID THM _Chem_comp.Provenance PDB _Chem_comp.Name THYMIDINE _Chem_comp.Type 'DNA OH 5 PRIME TERMINUS' _Chem_comp.BMRB_code THM _Chem_comp.PDB_code THM _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2017-08-21 _Chem_comp.Modified_date 2017-08-21 _Chem_comp.Release_status REL _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code . _Chem_comp.Three_letter_code THM _Chem_comp.Number_atoms_all 31 _Chem_comp.Number_atoms_nh 17 _Chem_comp.Atom_nomenclature_source . _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code ; InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1 ; _Chem_comp.Mon_nstd_flag . _Chem_comp.Mon_nstd_class . _Chem_comp.Mon_nstd_details . _Chem_comp.Mon_nstd_parent . _Chem_comp.Mon_nstd_parent_comp_ID . _Chem_comp.Std_deriv_one_letter_code . _Chem_comp.Std_deriv_three_letter_code . _Chem_comp.Std_deriv_BMRB_code . _Chem_comp.Std_deriv_PDB_code . _Chem_comp.Std_deriv_chem_comp_name . _Chem_comp.Synonyms "DEOXYTHYMIDINE; 2'-DEOXYTHYMIDINE" _Chem_comp.Formal_charge 0 _Chem_comp.Paramagnetic . _Chem_comp.Aromatic no _Chem_comp.Formula 'C10 H14 N2 O5' _Chem_comp.Formula_weight 242.229 _Chem_comp.Formula_mono_iso_wt_nat . _Chem_comp.Formula_mono_iso_wt_13C . _Chem_comp.Formula_mono_iso_wt_15N . _Chem_comp.Formula_mono_iso_wt_13C_15N . _Chem_comp.Image_file_name . _Chem_comp.Image_file_format . _Chem_comp.Topo_file_name . _Chem_comp.Topo_file_format . _Chem_comp.Struct_file_name . _Chem_comp.Struct_file_format . _Chem_comp.Stereochem_param_file_name . _Chem_comp.Stereochem_param_file_format . _Chem_comp.Model_details . _Chem_comp.Model_erf . _Chem_comp.Model_source . _Chem_comp.Model_coordinates_details . _Chem_comp.Model_coordinates_missing_flag no _Chem_comp.Ideal_coordinates_details . _Chem_comp.Ideal_coordinates_missing_flag no _Chem_comp.Model_coordinates_db_code 1KIM _Chem_comp.Processing_site EBI _Chem_comp.Vendor . _Chem_comp.Vendor_product_code . _Chem_comp.Details . _Chem_comp.DB_query_date . _Chem_comp.DB_last_query_revised_last_date . loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O SMILES 'OpenEye OEToolkits' 1.5.0 34162 THM CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 34162 THM CC1=CN([C@H]2C[C@H](O)[C@@H](CO)O2)C(=O)NC1=O SMILES_CANONICAL CACTVS 3.341 34162 THM CC1=CN([CH]2C[CH](O)[CH](CO)O2)C(=O)NC1=O SMILES CACTVS 3.341 34162 THM IQFYYKKMVGJFEH-XLPZGREQSA-N InChIKey InChI 1.03 34162 THM ; InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1 ; InChI InChI 1.03 34162 THM O=C1NC(=O)N(C=C1C)C2OC(C(O)C2)CO SMILES ACDLabs 10.04 34162 THM stop_ loop_ _Chem_comp_identifier.Identifier _Chem_comp_identifier.Type _Chem_comp_identifier.Program _Chem_comp_identifier.Program_version _Chem_comp_identifier.Entry_ID _Chem_comp_identifier.Comp_ID ; 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione ; 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 34162 THM thymidine 'SYSTEMATIC NAME' ACDLabs 10.04 34162 THM stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.BMRB_code _Chem_comp_atom.PDB_atom_ID _Chem_comp_atom.Alt_atom_ID _Chem_comp_atom.Auth_atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Isotope_number _Chem_comp_atom.Chirality _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Partial_charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Align _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.Leaving_atom_flag _Chem_comp_atom.Substruct_code _Chem_comp_atom.Ionizable _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_x_esd _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_y_esd _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.Model_Cartn_z_esd _Chem_comp_atom.Model_Cartn_x_ideal _Chem_comp_atom.Model_Cartn_y_ideal _Chem_comp_atom.Model_Cartn_z_ideal _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Details _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID O5' O5' O5' O5* . O . . N 0 . . . 1 no no . . . . 17.080 . 94.434 . 44.011 . 2.274 -0.724 -3.790 1 . 34162 THM C5' C5' C5' C5* . C . . N 0 . . . 1 no no . . . . 16.780 . 95.210 . 45.165 . 1.208 0.202 -3.574 2 . 34162 THM C4' C4' C4' C4* . C . . R 0 . . . 1 no no . . . . 17.626 . 96.447 . 45.302 . 0.116 -0.463 -2.735 3 . 34162 THM O4' O4' O4' O4* . O . . N 0 . . . 1 no no . . . . 18.982 . 96.128 . 45.630 . 0.600 -0.760 -1.406 4 . 34162 THM C3' C3' C3' C3* . C . . S 0 . . . 1 no no . . . . 17.760 . 97.332 . 44.178 . -1.055 0.519 -2.484 5 . 34162 THM O3' O3' O3' O3* . O . . N 0 . . . 1 no no . . . . 18.323 . 98.514 . 44.657 . -1.993 0.481 -3.562 6 . 34162 THM C2' C2' C2' C2* . C . . N 0 . . . 1 no no . . . . 18.903 . 96.738 . 43.506 . -1.681 -0.046 -1.186 7 . 34162 THM C1' C1' C1' C1* . C . . R 0 . . . 1 no no . . . . 19.875 . 96.449 . 44.597 . -0.554 -0.889 -0.560 8 . 34162 THM N1 N1 N1 N1 . N . . N 0 . . . 1 no no . . . . 20.731 . 95.216 . 44.411 . -0.246 -0.391 0.782 9 . 34162 THM C2 C2 C2 C2 . C . . N 0 . . . 1 no no . . . . 22.075 . 95.429 . 44.582 . 0.165 0.879 0.943 10 . 34162 THM O2 O2 O2 O2 . O . . N 0 . . . 1 no no . . . . 22.533 . 96.539 . 44.822 . 0.278 1.600 -0.029 11 . 34162 THM N3 N3 N3 N3 . N . . N 0 . . . 1 no no . . . . 22.877 . 94.370 . 44.420 . 0.454 1.363 2.165 12 . 34162 THM C4 C4 C4 C4 . C . . N 0 . . . 1 no no . . . . 22.432 . 93.082 . 44.088 . 0.329 0.578 3.254 13 . 34162 THM O4 O4 O4 O4 . O . . N 0 . . . 1 no no . . . . 23.259 . 92.155 . 43.945 . 0.590 1.015 4.360 14 . 34162 THM C5 C5 C5 C5 . C . . N 0 . . . 1 no no . . . . 20.989 . 92.899 . 43.924 . -0.098 -0.762 3.099 15 . 34162 THM C5M C5M C5M C5M . C . . N 0 . . . 1 no no . . . . 20.433 . 91.458 . 43.577 . -0.241 -1.662 4.299 16 . 34162 THM C6 C6 C6 C6 . C . . N 0 . . . 1 no no . . . . 20.205 . 93.954 . 44.081 . -0.382 -1.222 1.861 17 . 34162 THM HO5' HO5' HO5' *HO5 . H . . N 0 . . . 0 no no . . . . 16.545 . 93.653 . 43.924 . 2.939 -0.266 -4.322 18 . 34162 THM H5'1 H5'1 H5'1 1H5* . H . . N 0 . . . 0 no no . . . . 15.696 . 95.470 . 45.192 . 0.792 0.508 -4.534 19 . 34162 THM H5'2 H5'2 H5'2 2H5* . H . . N 0 . . . 0 no no . . . . 16.845 . 94.585 . 46.086 . 1.588 1.077 -3.047 20 . 34162 THM H4' H4' H4' H4* . H . . N 0 . . . 1 no no . . . . 17.039 . 96.972 . 46.091 . -0.241 -1.370 -3.222 21 . 34162 THM H3' H3' H3' H3* . H . . N 0 . . . 1 no no . . . . 16.814 . 97.484 . 43.606 . -0.686 1.532 -2.328 22 . 34162 THM HO3' HO3' HO3' *HO3 . H . . N 0 . . . 0 no no . . . . 18.411 . 99.099 . 43.913 . -2.738 1.040 -3.303 23 . 34162 THM H2'1 H2'1 H2'1 1H2* . H . . N 0 . . . 0 no no . . . . 18.649 . 95.852 . 42.877 . -2.542 -0.673 -1.420 24 . 34162 THM H2'2 H2'2 H2'2 2H2* . H . . N 0 . . . 0 no no . . . . 19.319 . 97.362 . 42.681 . -1.969 0.764 -0.517 25 . 34162 THM H1' H1' H1' H1* . H . . N 0 . . . 1 no no . . . . 20.593 . 97.293 . 44.715 . -0.859 -1.934 -0.506 26 . 34162 THM HN3 HN3 HN3 HN3 . H . . N 0 . . . 1 no no . . . . 23.871 . 94.552 . 44.555 . 0.750 2.281 2.263 27 . 34162 THM HM51 HM51 HM51 1HM5 . H . . N 0 . . . 0 no no . . . . 19.333 . 91.318 . 43.452 . 0.031 -1.112 5.200 28 . 34162 THM HM52 HM52 HM52 2HM5 . H . . N 0 . . . 0 no no . . . . 20.948 . 91.085 . 42.661 . -1.275 -1.999 4.378 29 . 34162 THM HM53 HM53 HM53 3HM5 . H . . N 0 . . . 0 no no . . . . 20.801 . 90.736 . 44.343 . 0.414 -2.525 4.186 30 . 34162 THM H6 H6 H6 H6 . H . . N 0 . . . 1 no no . . . . 19.124 . 93.783 . 43.938 . -0.713 -2.240 1.723 31 . 34162 THM stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 . SING O5' C5' no N 1 . 34162 THM 2 . SING O5' HO5' no N 2 . 34162 THM 3 . SING C5' C4' no N 3 . 34162 THM 4 . SING C5' H5'1 no N 4 . 34162 THM 5 . SING C5' H5'2 no N 5 . 34162 THM 6 . SING C4' O4' no N 6 . 34162 THM 7 . SING C4' C3' no N 7 . 34162 THM 8 . SING C4' H4' no N 8 . 34162 THM 9 . SING O4' C1' no N 9 . 34162 THM 10 . SING C3' O3' no N 10 . 34162 THM 11 . SING C3' C2' no N 11 . 34162 THM 12 . SING C3' H3' no N 12 . 34162 THM 13 . SING O3' HO3' no N 13 . 34162 THM 14 . SING C2' C1' no N 14 . 34162 THM 15 . SING C2' H2'1 no N 15 . 34162 THM 16 . SING C2' H2'2 no N 16 . 34162 THM 17 . SING C1' N1 no N 17 . 34162 THM 18 . SING C1' H1' no N 18 . 34162 THM 19 . SING N1 C2 no N 19 . 34162 THM 20 . SING N1 C6 no N 20 . 34162 THM 21 . DOUB C2 O2 no N 21 . 34162 THM 22 . SING C2 N3 no N 22 . 34162 THM 23 . SING N3 C4 no N 23 . 34162 THM 24 . SING N3 HN3 no N 24 . 34162 THM 25 . DOUB C4 O4 no N 25 . 34162 THM 26 . SING C4 C5 no N 26 . 34162 THM 27 . SING C5 C5M no N 27 . 34162 THM 28 . DOUB C5 C6 no N 28 . 34162 THM 29 . SING C5M HM51 no N 29 . 34162 THM 30 . SING C5M HM52 no N 30 . 34162 THM 31 . SING C5M HM53 no N 31 . 34162 THM 32 . SING C6 H6 no N 32 . 34162 THM stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID 34162 _Sample.ID 1 _Sample.Type solution _Sample.Sub_type . _Sample.Details '0.5 mM LL3, 90% H2O/10% D2O' _Sample.Aggregate_sample_number . _Sample.Solvent_system '90% H2O/10% D2O' _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 LL3 'natural abundance' . . 1 $entity_1 . . 0.5 . . mM . . . . 34162 1 2 NaPi 'natural abundance' . . . . . . 10 . . mM . . . . 34162 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_1 _Sample_condition_list.Entry_ID 34162 _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 'ionic strength' 10 . mM 34162 1 pH 7.0 . pH 34162 1 pressure 1 . atm 34162 1 temperature 278 . K 34162 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID 34162 _Software.ID 1 _Software.Type . _Software.Name AMBER _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . 34162 1 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID refinement 34162 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID 34162 _Software.ID 2 _Software.Type . _Software.Name CYANA _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'Guntert, Mumenthaler and Wuthrich' . . 34162 2 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'structure calculation' 34162 2 stop_ save_ save_software_3 _Software.Sf_category software _Software.Sf_framecode software_3 _Software.Entry_ID 34162 _Software.ID 3 _Software.Type . _Software.Name SPARKY _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID Goddard . . 34162 3 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID 'chemical shift assignment' 34162 3 stop_ save_ save_software_4 _Software.Sf_category software _Software.Sf_framecode software_4 _Software.Entry_ID 34162 _Software.ID 4 _Software.Type . _Software.Name TOPSPIN _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' . . 34162 4 stop_ loop_ _Task.Task _Task.Entry_ID _Task.Software_ID collection 34162 4 processing 34162 4 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 34162 _NMR_spectrometer.ID 1 _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model Avance _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 600 save_ save_NMR_spectrometer_list _NMR_spectrometer_list.Sf_category NMR_spectrometer_list _NMR_spectrometer_list.Sf_framecode NMR_spectrometer_list _NMR_spectrometer_list.Entry_ID 34162 _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 Bruker Avance . 600 . . . 34162 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 34162 _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 '2D 1H-1H NOESY' no . . . . . . . . . . 1 $sample_1 . . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 34162 1 2 '2D 1H-1H TOCSY' no . . . . . . . . . . 1 $sample_1 . . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 34162 1 3 '2D DQF-COSY' no . . . . . . . . . . 1 $sample_1 . . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . 34162 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference_1 _Chem_shift_reference.Entry_ID 34162 _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.Ref_correction_type _Chem_shift_ref.Correction_val _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID H 1 DSS 'methyl protons' . . . . ppm 0.000 internal direct 1.0 . . . . . 34162 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_assigned_chemical_shifts_1 _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts_1 _Assigned_chem_shift_list.Entry_ID 34162 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference_1 _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 '2D 1H-1H NOESY' . . . 34162 1 2 '2D 1H-1H TOCSY' . . . 34162 1 3 '2D DQF-COSY' . . . 34162 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.Ambiguity_set_ID _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 1 1 THM H1' H 1 6.47 0.00 . 1 . . . . A 1 THM H1' . 34162 1 2 . 1 1 1 1 THM H2'1 H 1 2.35 0.01 . . . . . . A 1 THM H2'1 . 34162 1 3 . 1 1 1 1 THM H2'2 H 1 2.53 0.00 . . . . . . A 1 THM H2'2 . 34162 1 4 . 1 1 1 1 THM H6 H 1 7.84 0.00 . 1 . . . . A 1 THM H6 . 34162 1 5 . 1 1 1 1 THM HM51 H 1 1.93 0.00 . 1 . . . . A 1 THM HM51 . 34162 1 6 . 1 1 1 1 THM HM52 H 1 1.93 0.00 . 1 . . . . A 1 THM HM52 . 34162 1 7 . 1 1 1 1 THM HM53 H 1 1.93 0.00 . 1 . . . . A 1 THM HM53 . 34162 1 8 . 1 1 1 1 THM HN3 H 1 11.40 0.00 . 1 . . . . A 1 THM HN3 . 34162 1 9 . 1 1 2 2 DNR H1' H 1 6.32 0.00 . 1 . . . . A 2 DNR H1' . 34162 1 10 . 1 1 2 2 DNR H2' H 1 1.06 0.00 . . . . . . A 2 DNR H2' . 34162 1 11 . 1 1 2 2 DNR H2'' H 1 2.26 0.00 . . . . . . A 2 DNR H2'' . 34162 1 12 . 1 1 2 2 DNR H5 H 1 6.11 0.01 . 1 . . . . A 2 DNR H5 . 34162 1 13 . 1 1 2 2 DNR H6 H 1 7.44 0.00 . 1 . . . . A 2 DNR H6 . 34162 1 14 . 1 1 2 2 DNR H41 H 1 7.28 0.00 . . . . . . A 2 DNR H41 . 34162 1 15 . 1 1 2 2 DNR H42 H 1 8.62 0.00 . . . . . . A 2 DNR H42 . 34162 1 16 . 1 1 3 3 DG H1 H 1 10.26 0.01 . 1 . . . . A 3 DG H1 . 34162 1 17 . 1 1 3 3 DG H1' H 1 5.94 0.01 . 1 . . . . A 3 DG H1' . 34162 1 18 . 1 1 3 3 DG H2' H 1 2.93 0.00 . . . . . . A 3 DG H2' . 34162 1 19 . 1 1 3 3 DG H2'' H 1 2.66 0.01 . . . . . . A 3 DG H2'' . 34162 1 20 . 1 1 3 3 DG H8 H 1 8.31 0.00 . 1 . . . . A 3 DG H8 . 34162 1 21 . 1 1 3 3 DG H21 H 1 5.84 0.00 . . . . . . A 3 DG H21 . 34162 1 22 . 1 1 3 3 DG H22 H 1 8.60 0.00 . . . . . . A 3 DG H22 . 34162 1 23 . 1 1 4 4 DT H1' H 1 6.13 0.00 . 1 . . . . A 4 DT H1' . 34162 1 24 . 1 1 4 4 DT H6 H 1 7.62 0.00 . 1 . . . . A 4 DT H6 . 34162 1 25 . 1 1 4 4 DT H71 H 1 1.75 0.01 . 1 . . . . A 4 DT H71 . 34162 1 26 . 1 1 4 4 DT H72 H 1 1.75 0.01 . 1 . . . . A 4 DT H72 . 34162 1 27 . 1 1 4 4 DT H73 H 1 1.75 0.01 . 1 . . . . A 4 DT H73 . 34162 1 28 . 1 1 6 6 DC H1' H 1 6.30 0.01 . 1 . . . . A 6 DC H1' . 34162 1 29 . 1 1 6 6 DC H2' H 1 2.44 0.00 . . . . . . A 6 DC H2' . 34162 1 30 . 1 1 6 6 DC H2'' H 1 2.44 0.00 . . . . . . A 6 DC H2'' . 34162 1 31 . 1 1 6 6 DC H5 H 1 6.13 0.00 . 1 . . . . A 6 DC H5 . 34162 1 32 . 1 1 6 6 DC H6 H 1 7.93 0.01 . 1 . . . . A 6 DC H6 . 34162 1 33 . 1 1 6 6 DC H41 H 1 7.46 0.01 . . . . . . A 6 DC H41 . 34162 1 34 . 1 1 6 6 DC H42 H 1 8.59 0.01 . . . . . . A 6 DC H42 . 34162 1 35 . 1 1 7 7 DNR H1' H 1 6.27 0.01 . 1 . . . . A 7 DNR H1' . 34162 1 36 . 1 1 7 7 DNR H2' H 1 0.78 0.01 . . . . . . A 7 DNR H2' . 34162 1 37 . 1 1 7 7 DNR H2'' H 1 2.09 0.00 . . . . . . A 7 DNR H2'' . 34162 1 38 . 1 1 7 7 DNR H5 H 1 5.95 0.01 . 1 . . . . A 7 DNR H5 . 34162 1 39 . 1 1 7 7 DNR H6 H 1 7.45 0.00 . 1 . . . . A 7 DNR H6 . 34162 1 40 . 1 1 7 7 DNR H41 H 1 8.19 0.00 . . . . . . A 7 DNR H41 . 34162 1 41 . 1 1 7 7 DNR H42 H 1 10.66 0.00 . . . . . . A 7 DNR H42 . 34162 1 42 . 1 1 8 8 DG H1 H 1 13.94 0.00 . 1 . . . . A 8 DG H1 . 34162 1 43 . 1 1 8 8 DG H1' H 1 6.03 0.01 . 1 . . . . A 8 DG H1' . 34162 1 44 . 1 1 8 8 DG H2' H 1 3.06 0.00 . . . . . . A 8 DG H2' . 34162 1 45 . 1 1 8 8 DG H2'' H 1 2.69 0.01 . . . . . . A 8 DG H2'' . 34162 1 46 . 1 1 8 8 DG H8 H 1 8.32 0.00 . 1 . . . . A 8 DG H8 . 34162 1 47 . 1 1 8 8 DG H21 H 1 7.63 0.01 . . . . . . A 8 DG H21 . 34162 1 48 . 1 1 8 8 DG H22 H 1 8.20 0.00 . . . . . . A 8 DG H22 . 34162 1 49 . 1 1 9 9 DT H1' H 1 5.93 0.00 . 1 . . . . A 9 DT H1' . 34162 1 50 . 1 1 9 9 DT H6 H 1 7.63 0.00 . 1 . . . . A 9 DT H6 . 34162 1 51 . 1 1 9 9 DT H71 H 1 1.69 0.00 . 1 . . . . A 9 DT H71 . 34162 1 52 . 1 1 9 9 DT H72 H 1 1.69 0.00 . 1 . . . . A 9 DT H72 . 34162 1 53 . 1 1 9 9 DT H73 H 1 1.69 0.00 . 1 . . . . A 9 DT H73 . 34162 1 54 . 1 1 10 10 DT H1' H 1 5.54 0.00 . 1 . . . . A 10 DT H1' . 34162 1 55 . 1 1 10 10 DT H6 H 1 7.76 0.00 . 1 . . . . A 10 DT H6 . 34162 1 56 . 1 1 11 11 DT H71 H 1 1.99 0.00 . 1 . . . . A 11 DT H71 . 34162 1 57 . 1 1 11 11 DT H72 H 1 1.99 0.00 . 1 . . . . A 11 DT H72 . 34162 1 58 . 1 1 11 11 DT H73 H 1 1.99 0.00 . 1 . . . . A 11 DT H73 . 34162 1 59 . 1 1 12 12 DT H6 H 1 7.84 0.00 . 1 . . . . A 12 DT H6 . 34162 1 60 . 1 1 12 12 DT H71 H 1 1.99 0.00 . 1 . . . . A 12 DT H71 . 34162 1 61 . 1 1 12 12 DT H72 H 1 1.99 0.00 . 1 . . . . A 12 DT H72 . 34162 1 62 . 1 1 12 12 DT H73 H 1 1.99 0.00 . 1 . . . . A 12 DT H73 . 34162 1 63 . 1 1 13 13 DT H1' H 1 6.12 0.01 . 1 . . . . A 13 DT H1' . 34162 1 64 . 1 1 13 13 DT H2' H 1 2.46 0.00 . . . . . . A 13 DT H2' . 34162 1 65 . 1 1 13 13 DT H2'' H 1 2.63 0.01 . . . . . . A 13 DT H2'' . 34162 1 66 . 1 1 13 13 DT H3 H 1 11.20 0.00 . 1 . . . . A 13 DT H3 . 34162 1 67 . 1 1 13 13 DT H6 H 1 7.74 0.00 . 1 . . . . A 13 DT H6 . 34162 1 68 . 1 1 13 13 DT H71 H 1 1.71 0.00 . 1 . . . . A 13 DT H71 . 34162 1 69 . 1 1 13 13 DT H72 H 1 1.71 0.00 . 1 . . . . A 13 DT H72 . 34162 1 70 . 1 1 13 13 DT H73 H 1 1.71 0.00 . 1 . . . . A 13 DT H73 . 34162 1 71 . 1 1 14 14 DC H1' H 1 6.41 0.00 . 1 . . . . A 14 DC H1' . 34162 1 72 . 1 1 14 14 DC H2' H 1 1.07 0.00 . . . . . . A 14 DC H2' . 34162 1 73 . 1 1 14 14 DC H2'' H 1 2.17 0.00 . . . . . . A 14 DC H2'' . 34162 1 74 . 1 1 14 14 DC H5 H 1 6.39 0.02 . 1 . . . . A 14 DC H5 . 34162 1 75 . 1 1 14 14 DC H6 H 1 7.49 0.00 . 1 . . . . A 14 DC H6 . 34162 1 76 . 1 1 14 14 DC H41 H 1 6.97 0.00 . . . . . . A 14 DC H41 . 34162 1 77 . 1 1 14 14 DC H42 H 1 8.66 0.01 . . . . . . A 14 DC H42 . 34162 1 78 . 1 1 15 15 DG H1' H 1 5.99 0.00 . 1 . . . . A 15 DG H1' . 34162 1 79 . 1 1 15 15 DG H2' H 1 2.99 0.00 . . . . . . A 15 DG H2' . 34162 1 80 . 1 1 15 15 DG H2'' H 1 2.70 0.00 . . . . . . A 15 DG H2'' . 34162 1 81 . 1 1 15 15 DG H8 H 1 8.39 0.00 . 1 . . . . A 15 DG H8 . 34162 1 82 . 1 1 15 15 DG H21 H 1 5.30 0.01 . . . . . . A 15 DG H21 . 34162 1 83 . 1 1 15 15 DG H22 H 1 9.07 0.01 . . . . . . A 15 DG H22 . 34162 1 84 . 1 1 16 16 DT H1' H 1 6.00 0.00 . 1 . . . . A 16 DT H1' . 34162 1 85 . 1 1 16 16 DT H6 H 1 7.64 0.00 . 1 . . . . A 16 DT H6 . 34162 1 86 . 1 1 16 16 DT H71 H 1 1.81 0.01 . 1 . . . . A 16 DT H71 . 34162 1 87 . 1 1 16 16 DT H72 H 1 1.81 0.01 . 1 . . . . A 16 DT H72 . 34162 1 88 . 1 1 16 16 DT H73 H 1 1.81 0.01 . 1 . . . . A 16 DT H73 . 34162 1 89 . 1 1 18 18 DC H1' H 1 6.30 0.00 . 1 . . . . A 18 DC H1' . 34162 1 90 . 1 1 18 18 DC H2' H 1 2.44 0.00 . . . . . . A 18 DC H2' . 34162 1 91 . 1 1 18 18 DC H2'' H 1 2.44 0.00 . . . . . . A 18 DC H2'' . 34162 1 92 . 1 1 18 18 DC H5 H 1 6.13 0.00 . 1 . . . . A 18 DC H5 . 34162 1 93 . 1 1 18 18 DC H6 H 1 7.93 0.01 . 1 . . . . A 18 DC H6 . 34162 1 94 . 1 1 18 18 DC H41 H 1 7.43 0.00 . . . . . . A 18 DC H41 . 34162 1 95 . 1 1 18 18 DC H42 H 1 8.55 0.00 . . . . . . A 18 DC H42 . 34162 1 96 . 1 1 19 19 DC H1' H 1 6.23 0.01 . 1 . . . . A 19 DC H1' . 34162 1 97 . 1 1 19 19 DC H2' H 1 0.76 0.00 . . . . . . A 19 DC H2' . 34162 1 98 . 1 1 19 19 DC H2'' H 1 2.02 0.00 . . . . . . A 19 DC H2'' . 34162 1 99 . 1 1 19 19 DC H3' H 1 4.70 0.00 . 1 . . . . A 19 DC H3' . 34162 1 100 . 1 1 19 19 DC H4' H 1 4.50 0.00 . 1 . . . . A 19 DC H4' . 34162 1 101 . 1 1 19 19 DC H5 H 1 5.95 0.01 . 1 . . . . A 19 DC H5 . 34162 1 102 . 1 1 19 19 DC H6 H 1 7.41 0.00 . 1 . . . . A 19 DC H6 . 34162 1 103 . 1 1 19 19 DC H41 H 1 8.05 0.00 . . . . . . A 19 DC H41 . 34162 1 104 . 1 1 19 19 DC H42 H 1 10.62 0.01 . . . . . . A 19 DC H42 . 34162 1 105 . 1 1 20 20 DG H1 H 1 13.65 0.00 . 1 . . . . A 20 DG H1 . 34162 1 106 . 1 1 20 20 DG H1' H 1 5.98 0.01 . 1 . . . . A 20 DG H1' . 34162 1 107 . 1 1 20 20 DG H2' H 1 3.04 0.00 . . . . . . A 20 DG H2' . 34162 1 108 . 1 1 20 20 DG H2'' H 1 2.66 0.00 . . . . . . A 20 DG H2'' . 34162 1 109 . 1 1 20 20 DG H8 H 1 8.27 0.00 . 1 . . . . A 20 DG H8 . 34162 1 110 . 1 1 20 20 DG H21 H 1 7.67 0.01 . . . . . . A 20 DG H21 . 34162 1 111 . 1 1 20 20 DG H22 H 1 7.96 0.00 . . . . . . A 20 DG H22 . 34162 1 112 . 1 1 21 21 DT H1' H 1 5.96 0.01 . 1 . . . . A 21 DT H1' . 34162 1 113 . 1 1 21 21 DT H6 H 1 7.63 0.00 . 1 . . . . A 21 DT H6 . 34162 1 114 . 1 1 21 21 DT H71 H 1 1.73 0.01 . 1 . . . . A 21 DT H71 . 34162 1 115 . 1 1 21 21 DT H72 H 1 1.73 0.01 . 1 . . . . A 21 DT H72 . 34162 1 116 . 1 1 21 21 DT H73 H 1 1.73 0.01 . 1 . . . . A 21 DT H73 . 34162 1 stop_ save_