data_1JRW # _entry.id 1JRW # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1JRW pdb_00001jrw 10.2210/pdb1jrw/pdb RCSB RCSB014117 ? ? WWPDB D_1000014117 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1QSK '1QSK contains a similar pentanucleotide DNA bulge with AAAAA in the bulge loop' unspecified PDB 1JRV '1JRV IS the SOLUTION STRUCTURE OF DAATAA DNA BULGE (ENSEMBLE)' unspecified PDB 1JS5 '1JS5 IS the AVERAGED SOLUTION STRUCTURE OF DAAUAA DNA BULGE' unspecified PDB 1JS7 '1JS7 IS the SOLUTION STRUCTURE (ENSEMBLE) OF DAAUAA DNA BULGE' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1JRW _pdbx_database_status.recvd_initial_deposition_date 2001-08-15 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Gollmick, F.A.' 1 'Lorenz, M.' 2 'Dornberger, U.' 3 'von Langen, J.' 4 'Diekmann, S.' 5 'Fritzsche, H.' 6 # _citation.id primary _citation.title 'Solution structure of dAATAA and dAAUAA DNA bulges.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 30 _citation.page_first 2669 _citation.page_last 2677 _citation.year 2002 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 12060684 _citation.pdbx_database_id_DOI 10.1093/nar/gkf375 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gollmick, F.A.' 1 ? primary 'Lorenz, M.' 2 ? primary 'Dornberger, U.' 3 ? primary 'von Langen, J.' 4 ? primary 'Diekmann, S.' 5 ? primary 'Fritzsche, H.' 6 ? # _cell.entry_id 1JRW _cell.length_a ? _cell.length_b ? _cell.length_c ? _cell.angle_alpha ? _cell.angle_beta ? _cell.angle_gamma ? _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "5'-D(*GP*CP*AP*TP*CP*GP*AP*AP*TP*AP*AP*GP*CP*TP*AP*CP*G)-3'" 5220.412 1 ? ? ? ? 2 polymer syn "5'-D(*CP*GP*TP*AP*GP*CP*CP*GP*AP*TP*GP*C)-3'" 3663.392 1 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 polydeoxyribonucleotide no no '(DG)(DC)(DA)(DT)(DC)(DG)(DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DA)(DC)(DG)' GCATCGAATAAGCTACG A ? 2 polydeoxyribonucleotide no no '(DC)(DG)(DT)(DA)(DG)(DC)(DC)(DG)(DA)(DT)(DG)(DC)' CGTAGCCGATGC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DA n 1 4 DT n 1 5 DC n 1 6 DG n 1 7 DA n 1 8 DA n 1 9 DT n 1 10 DA n 1 11 DA n 1 12 DG n 1 13 DC n 1 14 DT n 1 15 DA n 1 16 DC n 1 17 DG n 2 1 DC n 2 2 DG n 2 3 DT n 2 4 DA n 2 5 DG n 2 6 DC n 2 7 DC n 2 8 DG n 2 9 DA n 2 10 DT n 2 11 DG n 2 12 DC n # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1JRW 1JRW ? ? ? 2 2 PDB 1JRW 1JRW ? ? ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 1JRW A 1 ? 17 ? 1JRW 1 ? 17 ? 1 17 2 2 1JRW B 1 ? 12 ? 1JRW 18 ? 29 ? 18 29 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 2D_NOESY 2 1 1 E-COSY 3 2 1 31P-1H_correlated # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 300 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength '100mm Na+' _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system 1 '1.6mm in duplex; 10mm phosphate buffer; 100mm NaCl; 0.05mm EDTA; 100% D2O' '100% D2O' 2 '1.6mm in duplex; 100mm NaCl; 0.05mm EDTA; 100% D2O' '100% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Varian INOVA 500 2 ? Varian INOVA 600 3 ? Varian INOVA 750 # _pdbx_nmr_refine.entry_id 1JRW _pdbx_nmr_refine.method 'matrix relaxation; torsion angle dynamics; energy minimization' _pdbx_nmr_refine.details ;the structures are based on a total of 906 restraints, 645 are NOE-derived distance constraints, 235 dihedral angle restraints, 26 distance restraints from hydrogen bonds. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1JRW _pdbx_nmr_details.text ;THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. This structure was determined using standard 2D homonuclear and heteronuclear techniques. ; # _pdbx_nmr_ensemble.entry_id 1JRW _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 1JRW _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal NMRPipe 3 processing 'Delaglio, F., et al.' 1 MARDIGRAS 3.2 'iterative matrix relaxation' 'Borgias, B.A., James, T.L.' 2 DYANA 1.5 'structure solution' 'Guentert, P., Mumenthaler, C., Wuetrich, K.' 3 Amber 5.0 refinement 'WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A.' 4 Amber 5.0 'data analysis' 'WEINER, S.J., KOLLMAN, P.A., NGUYEN, D.T., CASE, D.A.' 5 # _exptl.entry_id 1JRW _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1JRW _struct.title 'Solution Structure of dAATAA DNA Bulge' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1JRW _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA BULGE, five-nucleotide bulge loop, deoxyribonucleic acid, DNA' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 2 B DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 2 B DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 2 B DG 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 3 B DT 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 3 B DT 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 9 N1 ? ? A DT 4 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 9 N6 ? ? A DT 4 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 5 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 5 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 5 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 6 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 6 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 6 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 12 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 12 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 12 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 13 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 13 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 13 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 14 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 14 B DA 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 14 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 14 B DA 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 15 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 15 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 15 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 15 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 16 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 16 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 16 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 16 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 16 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 16 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 17 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 17 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 17 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 17 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 17 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 17 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1JRW _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1JRW _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C H N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG GUA A . n A 1 2 DC 2 2 2 DC CYT A . n A 1 3 DA 3 3 3 DA ADE A . n A 1 4 DT 4 4 4 DT THY A . n A 1 5 DC 5 5 5 DC CYT A . n A 1 6 DG 6 6 6 DG GUA A . n A 1 7 DA 7 7 7 DA ADE A . n A 1 8 DA 8 8 8 DA ADE A . n A 1 9 DT 9 9 9 DT THY A . n A 1 10 DA 10 10 10 DA ADE A . n A 1 11 DA 11 11 11 DA ADE A . n A 1 12 DG 12 12 12 DG GUA A . n A 1 13 DC 13 13 13 DC CYT A . n A 1 14 DT 14 14 14 DT THY A . n A 1 15 DA 15 15 15 DA ADE A . n A 1 16 DC 16 16 16 DC CYT A . n A 1 17 DG 17 17 17 DG GUA A . n B 2 1 DC 1 18 18 DC CYT B . n B 2 2 DG 2 19 19 DG GUA B . n B 2 3 DT 3 20 20 DT THY B . n B 2 4 DA 4 21 21 DA ADE B . n B 2 5 DG 5 22 22 DG GUA B . n B 2 6 DC 6 23 23 DC CYT B . n B 2 7 DC 7 24 24 DC CYT B . n B 2 8 DG 8 25 25 DG GUA B . n B 2 9 DA 9 26 26 DA ADE B . n B 2 10 DT 10 27 27 DT THY B . n B 2 11 DG 11 28 28 DG GUA B . n B 2 12 DC 12 29 29 DC CYT B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2002-08-28 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 110.45 108.30 2.15 0.30 N 2 1 "O4'" A DA 3 ? ? "C4'" A DA 3 ? ? "C3'" A DA 3 ? ? 111.75 106.00 5.75 0.60 N 3 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 110.55 108.30 2.25 0.30 N 4 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 118.01 122.90 -4.89 0.60 N 5 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.88 108.30 2.58 0.30 N 6 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? N9 A DA 7 ? ? 112.93 108.30 4.63 0.30 N 7 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 114.67 108.30 6.37 0.30 N 8 1 "O4'" A DA 11 ? ? "C1'" A DA 11 ? ? N9 A DA 11 ? ? 113.50 108.30 5.20 0.30 N 9 1 "O4'" A DC 13 ? ? "C4'" A DC 13 ? ? "C3'" A DC 13 ? ? 110.78 106.00 4.78 0.60 N 10 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 111.08 108.30 2.78 0.30 N 11 1 "O4'" B DA 26 ? ? "C4'" B DA 26 ? ? "C3'" B DA 26 ? ? 109.81 106.00 3.81 0.60 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA A 3 ? ? 0.059 'SIDE CHAIN' 2 1 DC B 18 ? ? 0.086 'SIDE CHAIN' 3 1 DG B 19 ? ? 0.086 'SIDE CHAIN' 4 1 DG B 25 ? ? 0.063 'SIDE CHAIN' 5 1 DT B 27 ? ? 0.061 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1JRW 'double helix' 1JRW 'b-form double helix' 1JRW 'bulge loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 2 1_555 B DG 11 1_555 -0.223 -0.046 -0.077 -0.074 8.348 -3.576 1 A_DC2:DG28_B A 2 ? B 28 ? 19 1 1 A DA 3 1_555 B DT 10 1_555 -0.429 -0.107 0.129 0.624 -11.465 5.187 2 A_DA3:DT27_B A 3 ? B 27 ? 20 1 1 A DT 4 1_555 B DA 9 1_555 -0.033 -0.146 0.656 -12.544 -14.075 -1.988 3 A_DT4:DA26_B A 4 ? B 26 ? 20 1 1 A DC 5 1_555 B DG 8 1_555 -0.209 0.052 0.265 -13.881 -12.635 -1.484 4 A_DC5:DG25_B A 5 ? B 25 ? 19 1 1 A DG 6 1_555 B DC 7 1_555 0.253 -0.100 0.645 -8.485 5.445 -2.101 5 A_DG6:DC24_B A 6 ? B 24 ? 19 1 1 A DG 12 1_555 B DC 6 1_555 -0.166 -0.030 0.286 11.670 13.913 -1.809 6 A_DG12:DC23_B A 12 ? B 23 ? 19 1 1 A DC 13 1_555 B DG 5 1_555 -0.387 -0.123 0.955 -6.933 -3.841 -2.388 7 A_DC13:DG22_B A 13 ? B 22 ? 19 1 1 A DT 14 1_555 B DA 4 1_555 0.234 -0.140 0.536 5.182 -3.342 -8.217 8 A_DT14:DA21_B A 14 ? B 21 ? 20 1 1 A DA 15 1_555 B DT 3 1_555 -0.471 -0.198 0.667 9.329 -7.136 0.492 9 A_DA15:DT20_B A 15 ? B 20 ? 20 1 1 A DC 16 1_555 B DG 2 1_555 0.091 -0.064 0.454 -0.184 -1.287 -0.530 10 A_DC16:DG19_B A 16 ? B 19 ? 19 1 1 A DG 17 1_555 B DC 1 1_555 1.278 -0.566 -1.630 13.891 7.118 -12.919 11 A_DG17:DC18_B A 17 ? B 18 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 2 1_555 B DG 11 1_555 A DA 3 1_555 B DT 10 1_555 -0.213 0.195 3.208 -4.197 12.121 36.267 -1.211 -0.199 3.118 18.764 6.498 38.396 1 AA_DC2DA3:DT27DG28_BB A 2 ? B 28 ? A 3 ? B 27 ? 1 A DA 3 1_555 B DT 10 1_555 A DT 4 1_555 B DA 9 1_555 -0.588 -0.677 3.507 -4.733 0.687 31.129 -1.386 0.126 3.540 1.271 8.755 31.485 2 AA_DA3DT4:DA26DT27_BB A 3 ? B 27 ? A 4 ? B 26 ? 1 A DT 4 1_555 B DA 9 1_555 A DC 5 1_555 B DG 8 1_555 0.411 0.028 3.106 5.844 6.509 35.087 -0.838 0.132 3.089 10.595 -9.512 36.127 3 AA_DT4DC5:DG25DA26_BB A 4 ? B 26 ? A 5 ? B 25 ? 1 A DC 5 1_555 B DG 8 1_555 A DG 6 1_555 B DC 7 1_555 -0.216 0.483 3.413 -4.095 13.750 31.459 -1.494 -0.322 3.332 23.867 7.108 34.501 4 AA_DC5DG6:DC24DG25_BB A 5 ? B 25 ? A 6 ? B 24 ? 1 A DG 12 1_555 B DC 6 1_555 A DC 13 1_555 B DG 5 1_555 -0.250 -0.866 3.786 -5.159 1.743 37.659 -1.585 -0.374 3.744 2.683 7.941 38.037 5 AA_DG12DC13:DG22DC23_BB A 12 ? B 23 ? A 13 ? B 22 ? 1 A DC 13 1_555 B DG 5 1_555 A DT 14 1_555 B DA 4 1_555 -0.412 -0.459 2.910 3.788 1.159 30.385 -1.069 1.437 2.820 2.200 -7.189 30.636 6 AA_DC13DT14:DA21DG22_BB A 13 ? B 22 ? A 14 ? B 21 ? 1 A DT 14 1_555 B DA 4 1_555 A DA 15 1_555 B DT 3 1_555 0.115 -0.117 3.189 -0.933 18.468 33.771 -2.424 -0.288 2.761 29.231 1.477 38.373 7 AA_DT14DA15:DT20DA21_BB A 14 ? B 21 ? A 15 ? B 20 ? 1 A DA 15 1_555 B DT 3 1_555 A DC 16 1_555 B DG 2 1_555 0.078 -0.543 3.477 -0.495 0.968 33.079 -1.127 -0.225 3.459 1.699 0.869 33.097 8 AA_DA15DC16:DG19DT20_BB A 15 ? B 20 ? A 16 ? B 19 ? 1 A DC 16 1_555 B DG 2 1_555 A DG 17 1_555 B DC 1 1_555 -0.053 0.229 3.555 10.813 0.524 37.045 0.276 1.536 3.410 0.805 -16.589 38.541 9 AA_DC16DG17:DC18DG19_BB A 16 ? B 19 ? A 17 ? B 18 ? #