data_1QL5 # _entry.id 1QL5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.321 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1QL5 PDBE EBI-2968 WWPDB D_1290002968 BMRB 4412 # _pdbx_database_related.db_id 4412 _pdbx_database_related.details . _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1QL5 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 1999-08-24 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs REL # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Lee, J.-H.' 1 ? 'Hwang, G.-S.' 2 ? 'Choi, B.-S.' 3 ? # _citation.id primary _citation.title ;Solution Structure of a DNA Decamer Duplex Containing the 3' T.T Base Pair of the Cis-Syn Cyclobutane Pyrimidine Dimer: Implication for the Mutagenic Property of the Cis-Syn Dimer. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 28 _citation.page_first 1794 _citation.page_last ? _citation.year 2000 _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 10734199 _citation.pdbx_database_id_DOI 10.1093/NAR/28.8.1794 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lee, J.-H.' 1 ? primary 'Choi, Y.-J.' 2 ? primary 'Choi, B.-S.' 3 ? # _cell.entry_id 1QL5 _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1QL5 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # 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 ;DNA (5'-D(*CP*GP*CP*AP*TP*+TP*AP*CP*GP*C)- 3') ; 3009.013 1 ? ? ? 'CYCLOBUTANE RING FORMED BETWEEN C5-C6(T5) AND C5-C6(T6) DOUBLE BONDS' 2 polymer syn ;DNA (5'-D(*GP*CP*GP*TP*TP*AP*TP*GP*CP*G)-3') ; 3076.015 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 yes '(DC)(DG)(DC)(DA)(PBT)(PBT)(DA)(DC)(DG)(DC)' CGCANNACGC A ? 2 polydeoxyribonucleotide no no '(DG)(DC)(DG)(DT)(DT)(DA)(DT)(DG)(DC)(DG)' GCGTTATGCG B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DA n 1 5 PBT n 1 6 PBT n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC n 2 1 DG n 2 2 DC n 2 3 DG n 2 4 DT n 2 5 DT n 2 6 DA n 2 7 DT n 2 8 DG n 2 9 DC n 2 10 DG n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 1QL5 1 ? ? 1QL5 ? 2 PDB 1QL5 2 ? ? 1QL5 ? # 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 1QL5 A 1 ? 10 ? 1QL5 1 ? 10 ? 1 10 2 2 1QL5 B 1 ? 10 ? 1QL5 11 ? 20 ? 11 20 # 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 PBT 'DNA linking' . '[3-HYDROXY-5-(5-METHYL-2,4-DIOXOTETRAHYDRO-1(2H)-PYRIMIDINYL)TETRAHYDRO-2-FURANYL]METHYL DIHYDROGEN PHOSPHATE' ? 'C10 H17 N2 O8 P' 324.224 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type NOESY _pdbx_nmr_exptl.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 274.0 _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.6 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model DMX _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1QL5 _pdbx_nmr_refine.method 'SIMULATED ANNEALING AND FULL RELAXATION MATRIX REFINEMENT' _pdbx_nmr_refine.details ;MISMATCHED BASE PAIRING OF 3'-T OF CIS-SYN DIMER WITH A RESIDUE. REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1QL5 _pdbx_nmr_details.text ;MEAN STRUCTURE. THE STRUCTURE WAS DETERMINED USING SA METHOD WITH DISTANCE RESTRAINTS AND FULL RELAXATION MATRIX REFINEMENT WITH NOE INTENSITY RESTRAINTS OF 50, 80, 160 MS MIXING TIMES ; # _pdbx_nmr_ensemble.entry_id 1QL5 _pdbx_nmr_ensemble.conformers_calculated_total_number 8 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'LEAST RESTRAINT VIOLATION' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR ? ? 2 # _exptl.entry_id 1QL5 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1QL5 _struct.title 'DNA DECAMER DUPLEX CONTAINING T5-T6 PHOTOADDUCT' _struct.pdbx_descriptor "5'-D(*CP*GP*CP*AP*(PBT)P*(PBT)P*AP*CP*GP*C)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'MINIMIZED AVERAGE' # _struct_keywords.entry_id 1QL5 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, DEOXYRIBONUCLEIC ACID, DNA PHOTOPRODUCT, (6-4) ADDUCT, MUTAGENESIS' # 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 ? # 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 covale1 covale both ? A DA 4 "O3'" ? ? ? 1_555 A PBT 5 P ? ? A DA 4 A PBT 5 1_555 ? ? ? ? ? ? ? 1.597 ? covale2 covale one ? A PBT 5 "O3'" ? ? ? 1_555 A PBT 6 P ? ? A PBT 5 A PBT 6 1_555 ? ? ? ? ? ? ? 1.610 ? covale3 covale none ? A PBT 5 C5 ? ? ? 1_555 A PBT 6 C5 ? ? A PBT 5 A PBT 6 1_555 ? ? ? ? ? ? ? 1.653 ? covale4 covale none ? A PBT 5 C6 ? ? ? 1_555 A PBT 6 C6 ? ? A PBT 5 A PBT 6 1_555 ? ? ? ? ? ? ? 1.657 ? covale5 covale one ? A PBT 6 "O3'" ? ? ? 1_555 A DA 7 P ? ? A PBT 6 A DA 7 1_555 ? ? ? ? ? ? ? 1.619 ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 1 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 2 B DC 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 3 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 4 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 8 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 9 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 10 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1QL5 _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 1QL5 _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 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 PBT 5 5 5 PBT PBT A . n A 1 6 PBT 6 6 6 PBT PBT A . n A 1 7 DA 7 7 7 DA DA A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DC 10 10 10 DC DC A . n B 2 1 DG 1 11 11 DG DG B . n B 2 2 DC 2 12 12 DC DC B . n B 2 3 DG 3 13 13 DG DG B . n B 2 4 DT 4 14 14 DT DT B . n B 2 5 DT 5 15 15 DT DT B . n B 2 6 DA 6 16 16 DA DA B . n B 2 7 DT 7 17 17 DT DT B . n B 2 8 DG 8 18 18 DG DG B . n B 2 9 DC 9 19 19 DC DC B . n B 2 10 DG 10 20 20 DG DG B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 2040 ? 1 MORE 5 ? 1 'SSA (A^2)' 3620 ? # _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 2000-04-10 2 'Structure model' 1 1 2012-02-22 3 'Structure model' 1 2 2020-01-15 # _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' 'Database references' 2 2 'Structure model' 'Derived calculations' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' Other # 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 3 'Structure model' pdbx_database_status 2 3 'Structure model' struct_conn # 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 3 'Structure model' '_pdbx_database_status.status_code_cs' 2 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 "HO5'" _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DC _pdbx_validate_close_contact.auth_seq_id_1 1 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 OP1 _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 DG _pdbx_validate_close_contact.auth_seq_id_2 2 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.55 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 N9 B DA 16 ? ? C4 B DA 16 ? ? 1.413 1.374 0.039 0.006 N 2 1 N1 B DT 17 ? ? C2 B DT 17 ? ? 1.430 1.376 0.054 0.008 N # 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 DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.64 108.30 4.34 0.30 N 2 1 N1 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 122.59 118.90 3.69 0.60 N 3 1 "C3'" A DG 2 ? ? "O3'" A DG 2 ? ? P A DC 3 ? ? 136.57 119.70 16.87 1.20 Y 4 1 N1 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 122.85 118.90 3.95 0.60 N 5 1 "C3'" A DC 3 ? ? "O3'" A DC 3 ? ? P A DA 4 ? ? 128.51 119.70 8.81 1.20 Y 6 1 "C3'" A DA 4 ? ? "O3'" A DA 4 ? ? P A PBT 5 ? ? 131.48 119.70 11.78 1.20 Y 7 1 "C3'" A PBT 5 ? ? "O3'" A PBT 5 ? ? P A PBT 6 ? ? 143.67 119.70 23.97 1.20 Y 8 1 N1 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 122.79 118.90 3.89 0.60 N 9 1 "C3'" A DC 8 ? ? "O3'" A DC 8 ? ? P A DG 9 ? ? 129.28 119.70 9.58 1.20 Y 10 1 "C3'" A DG 9 ? ? "O3'" A DG 9 ? ? P A DC 10 ? ? 131.61 119.70 11.91 1.20 Y 11 1 N3 B DG 11 ? ? C2 B DG 11 ? ? N2 B DG 11 ? ? 124.81 119.90 4.91 0.70 N 12 1 N1 B DC 12 ? ? C2 B DC 12 ? ? O2 B DC 12 ? ? 122.86 118.90 3.96 0.60 N 13 1 "C3'" B DC 12 ? ? "O3'" B DC 12 ? ? P B DG 13 ? ? 127.07 119.70 7.37 1.20 Y 14 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 110.50 108.30 2.20 0.30 N 15 1 C2 B DG 13 ? ? N3 B DG 13 ? ? C4 B DG 13 ? ? 115.53 111.90 3.63 0.50 N 16 1 "C3'" B DG 13 ? ? "O3'" B DG 13 ? ? P B DT 14 ? ? 128.63 119.70 8.93 1.20 Y 17 1 "C3'" B DT 14 ? ? "C2'" B DT 14 ? ? "C1'" B DT 14 ? ? 96.78 102.40 -5.62 0.80 N 18 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 111.94 108.30 3.64 0.30 N 19 1 "C3'" B DT 14 ? ? "O3'" B DT 14 ? ? P B DT 15 ? ? 133.15 119.70 13.45 1.20 Y 20 1 "C3'" B DT 15 ? ? "O3'" B DT 15 ? ? P B DA 16 ? ? 127.36 119.70 7.66 1.20 Y 21 1 "C3'" B DA 16 ? ? "O3'" B DA 16 ? ? P B DT 17 ? ? 132.29 119.70 12.59 1.20 Y 22 1 C2 B DG 18 ? ? N3 B DG 18 ? ? C4 B DG 18 ? ? 115.21 111.90 3.31 0.50 N 23 1 "C3'" B DG 18 ? ? "O3'" B DG 18 ? ? P B DC 19 ? ? 131.29 119.70 11.59 1.20 Y 24 1 P B DG 20 ? ? "O5'" B DG 20 ? ? "C5'" B DG 20 ? ? 133.23 120.90 12.33 1.60 N # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id C5 _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id A _pdbx_validate_chiral.auth_comp_id PBT _pdbx_validate_chiral.auth_seq_id 5 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details 'WRONG HAND' _pdbx_validate_chiral.omega . # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1QL5 'double helix' 1QL5 'b-form double helix' # 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 1 1_555 B DG 10 1_555 0.361 -0.209 0.006 -2.070 -1.929 -4.486 1 A_DC1:DG20_B A 1 ? B 20 ? 19 1 1 A DG 2 1_555 B DC 9 1_555 0.333 -0.068 0.581 12.342 -0.952 -4.855 2 A_DG2:DC19_B A 2 ? B 19 ? 19 1 1 A DC 3 1_555 B DG 8 1_555 0.046 -0.157 -0.013 2.285 -1.523 -6.116 3 A_DC3:DG18_B A 3 ? B 18 ? 19 1 1 A DA 4 1_555 B DT 7 1_555 0.310 -0.087 -0.140 2.955 -13.746 -5.876 4 A_DA4:DT17_B A 4 ? B 17 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.013 -0.084 0.123 5.877 -2.649 -0.150 5 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B DG 3 1_555 0.038 -0.164 0.207 0.117 7.102 -4.147 6 A_DC8:DG13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B DC 2 1_555 -0.051 -0.146 -0.471 1.034 -3.165 -5.516 7 A_DG9:DC12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B DG 1 1_555 0.345 -0.182 0.059 -9.696 6.068 -5.256 8 A_DC10:DG11_B A 10 ? B 11 ? 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 1 1_555 B DG 10 1_555 A DG 2 1_555 B DC 9 1_555 -0.767 1.228 3.165 -6.727 1.910 32.937 1.809 0.225 3.317 3.322 11.701 33.651 1 AA_DC1DG2:DC19DG20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DG 2 1_555 B DC 9 1_555 A DC 3 1_555 B DG 8 1_555 0.027 -1.004 3.535 3.631 2.399 33.739 -2.126 0.574 3.442 4.112 -6.223 34.011 2 AA_DG2DC3:DG18DC19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DC 3 1_555 B DG 8 1_555 A DA 4 1_555 B DT 7 1_555 0.188 0.753 3.281 1.970 0.748 46.936 0.883 -0.072 3.297 0.938 -2.472 46.981 3 AA_DC3DA4:DT17DG18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B DG 3 1_555 -1.025 -0.793 3.549 -2.733 -3.560 36.276 -0.721 1.217 3.672 -5.690 4.368 36.543 4 AA_DA7DC8:DG13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B DG 3 1_555 A DG 9 1_555 B DC 2 1_555 -0.173 -1.686 3.212 5.385 3.533 29.740 -3.885 1.352 2.921 6.783 -10.338 30.414 5 AA_DC8DG9:DC12DG13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B DC 2 1_555 A DC 10 1_555 B DG 1 1_555 0.019 -1.341 3.728 -5.478 -5.222 40.644 -1.247 -0.713 3.830 -7.439 7.804 41.313 6 AA_DG9DC10:DG11DC12_BB A 9 ? B 12 ? A 10 ? B 11 ? #