data_1JDG # _entry.id 1JDG # _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 1JDG pdb_00001jdg 10.2210/pdb1jdg/pdb RCSB RCSB013650 ? ? WWPDB D_1000013650 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1JDG _pdbx_database_status.recvd_initial_deposition_date 2001-06-13 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.pdb_format_compatible Y _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 'Pradhan, P.' 1 'Tirumala, S.' 2 'Liu, X.' 3 'Sayer, J.M.' 4 'Jerina, D.M.' 5 'Yeh, H.J.C.' 6 # _citation.id primary _citation.title ;Solution structure of a trans-opened (10S)-dA adduct of (+)-(7S,8R,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully complementary DNA duplex: evidence for a major syn conformation. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 40 _citation.page_first 5870 _citation.page_last 5881 _citation.year 2001 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11352722 _citation.pdbx_database_id_DOI 10.1021/bi002896q # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Pradhan, P.' 1 ? primary 'Tirumala, S.' 2 ? primary 'Liu, X.' 3 ? primary 'Sayer, J.M.' 4 ? primary 'Jerina, D.M.' 5 ? primary 'Yeh, H.J.' 6 ? # 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(*CP*GP*GP*TP*CP*(BPA)AP*CP*GP*AP*GP*G)-3'" 3399.223 1 ? ? ? ? 2 polymer syn "5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3'" 3310.161 1 ? ? ? ? 3 non-polymer syn '7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE' 304.339 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 '(DC)(DG)(DG)(DT)(DC)(DA)(DC)(DG)(DA)(DG)(DG)' CGGTCACGAGG A ? 2 polydeoxyribonucleotide no no '(DC)(DC)(DT)(DC)(DG)(DT)(DG)(DA)(DC)(DC)(DG)' CCTCGTGACCG 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 DG n 1 4 DT n 1 5 DC n 1 6 DA n 1 7 DC n 1 8 DG n 1 9 DA n 1 10 DG n 1 11 DG n 2 1 DC n 2 2 DC n 2 3 DT n 2 4 DC n 2 5 DG n 2 6 DT n 2 7 DG n 2 8 DA n 2 9 DC n 2 10 DC n 2 11 DG 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 1JDG 1JDG ? ? ? 2 2 PDB 1JDG 1JDG ? ? ? # 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 1JDG A 1 ? 11 ? 1JDG 1 ? 11 ? 1 11 2 2 1JDG B 1 B 11 B 1JDG 1 ? 11 ? 1 11 # 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 BPA non-polymer . '7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE' ? 'C20 H16 O3' 304.339 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 NOESY 2 1 1 TOCSY 3 1 1 ROESY # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.8 _pdbx_nmr_exptl_sample_conditions.ionic_strength 0.1M _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '2mM DNA' _pdbx_nmr_sample_details.solvent_system ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model VXRS _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1JDG _pdbx_nmr_refine.method ;Simulated Annealing, Restraint Molecular Dynamics, Relaxation Matrix Analysis ; _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1JDG _pdbx_nmr_ensemble.conformers_calculated_total_number 11 _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 ? # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal Discover 3.0 refinement 'Weiner, S.' 1 Felix 2000 processing ? 2 IRMA 2000 'iterative matrix relaxation' ? 3 'Insight II' ? 'data analysis' ? 4 # _exptl.entry_id 1JDG _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1JDG _struct.title ;Solution Structure of a Trans-Opened (10S)-dA Adduct of (+)-(7S,8R,9S,10R)-7,8-Dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in a fully Complementary DNA Duplex ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1JDG _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'syn glycosidic torsion angle, benzo[a]pyrene diol epoxide, dA adduct, 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 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # 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 covale1 covale none ? A DA 6 N6 ? ? ? 1_555 C BPA . C10 ? ? A DA 6 A BPA 12 1_555 ? ? ? ? ? ? ? 1.479 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 11 N1 ? B A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 11 O6 ? B A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 11 N2 ? B A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 10 N3 ? B A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 10 O2 ? B A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 10 N4 ? B A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 9 N3 ? B A DG 3 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 9 O2 ? B A DG 3 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 9 N4 ? B A DG 3 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 8 N1 ? B A DT 4 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 8 N6 ? B A DT 4 B DA 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 7 N1 ? B A DC 5 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 7 O6 ? B A DC 5 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 7 N2 ? B A DC 5 B DG 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 6 O4 ? B A DA 6 B DT 6 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 5 N1 ? B A DC 7 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 5 O6 ? B A DC 7 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 5 N2 ? B A DC 7 B DG 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 4 N3 ? B A DG 8 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 4 O2 ? B A DG 8 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 4 N4 ? B A DG 8 B DC 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 3 N3 ? B A DA 9 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 3 O4 ? B A DA 9 B DT 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 2 N3 ? B A DG 10 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 2 O2 ? B A DG 10 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 2 N4 ? B A DG 10 B DC 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? B A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? B A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? B A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id BPA _struct_site.pdbx_auth_seq_id 12 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 4 _struct_site.details 'BINDING SITE FOR RESIDUE BPA A 12' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 4 DC A 7 ? DC A 7 . ? 1_555 ? 3 AC1 4 DG B 5 B DG B 5 . ? 1_555 ? 4 AC1 4 DT B 6 B DT B 6 . ? 1_555 ? # _database_PDB_matrix.entry_id 1JDG _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 1JDG _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 CYT A . n A 1 2 DG 2 2 2 DG GUA A . n A 1 3 DG 3 3 3 DG GUA 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 DA 6 6 6 DA ABP A . n A 1 7 DC 7 7 7 DC CYT A . n A 1 8 DG 8 8 8 DG GUA A . n A 1 9 DA 9 9 9 DA ADE A . n A 1 10 DG 10 10 10 DG GUA A . n A 1 11 DG 11 11 11 DG GUA A . n B 2 1 DC 1 1 1 DC CYT B B n B 2 2 DC 2 2 2 DC CYT B B n B 2 3 DT 3 3 3 DT THY B B n B 2 4 DC 4 4 4 DC CYT B B n B 2 5 DG 5 5 5 DG GUA B B n B 2 6 DT 6 6 6 DT THY B B n B 2 7 DG 7 7 7 DG GUA B B n B 2 8 DA 8 8 8 DA ADE B B n B 2 9 DC 9 9 9 DC CYT B B n B 2 10 DC 10 10 10 DC CYT B B n B 2 11 DG 11 11 11 DG GUA B B n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id BPA _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 12 _pdbx_nonpoly_scheme.auth_seq_num 6 _pdbx_nonpoly_scheme.pdb_mon_id BPA _pdbx_nonpoly_scheme.auth_mon_id ABP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _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,C # _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 2001-07-04 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 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # 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' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 6 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 7 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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 ? ? 111.27 108.30 2.97 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.37 108.30 3.07 0.30 N 3 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 110.32 108.30 2.02 0.30 N 4 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.36 108.30 3.06 0.30 N 5 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 110.74 108.30 2.44 0.30 N 6 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 114.25 108.30 5.95 0.30 N 7 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.83 108.30 3.53 0.30 N 8 1 "O4'" A DA 9 ? ? "C1'" A DA 9 ? ? N9 A DA 9 ? ? 111.58 108.30 3.28 0.30 N 9 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 111.66 108.30 3.36 0.30 N 10 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 111.42 108.30 3.12 0.30 N 11 1 "O4'" B DC 1 B ? "C1'" B DC 1 B ? N1 B DC 1 B ? 111.24 108.30 2.94 0.30 N 12 1 "O4'" B DC 2 B ? "C1'" B DC 2 B ? N1 B DC 2 B ? 111.73 108.30 3.43 0.30 N 13 1 "O4'" B DT 3 B ? "C1'" B DT 3 B ? N1 B DT 3 B ? 111.31 108.30 3.01 0.30 N 14 1 "O4'" B DC 4 B ? "C1'" B DC 4 B ? N1 B DC 4 B ? 111.30 108.30 3.00 0.30 N 15 1 "O4'" B DG 5 B ? "C1'" B DG 5 B ? N9 B DG 5 B ? 113.06 108.30 4.76 0.30 N 16 1 "O4'" B DT 6 B ? "C1'" B DT 6 B ? N1 B DT 6 B ? 112.07 108.30 3.77 0.30 N 17 1 "O4'" B DG 7 B ? "C1'" B DG 7 B ? N9 B DG 7 B ? 110.60 108.30 2.30 0.30 N 18 1 "O4'" B DA 8 B ? "C1'" B DA 8 B ? N9 B DA 8 B ? 111.05 108.30 2.75 0.30 N 19 1 "O4'" B DC 9 B ? "C1'" B DC 9 B ? N1 B DC 9 B ? 111.30 108.30 3.00 0.30 N 20 1 "O4'" B DC 10 B ? "C1'" B DC 10 B ? N1 B DC 10 B ? 111.18 108.30 2.88 0.30 N 21 1 "O4'" B DG 11 B ? "C1'" B DG 11 B ? N9 B DG 11 B ? 111.06 108.30 2.76 0.30 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 DG A 3 ? ? 0.081 'SIDE CHAIN' 2 1 DT A 4 ? ? 0.092 'SIDE CHAIN' 3 1 DC A 5 ? ? 0.083 'SIDE CHAIN' 4 1 DT B 3 B ? 0.068 'SIDE CHAIN' 5 1 DG B 11 B ? 0.061 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1JDG 'double helix' 1JDG '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 11 1_555 -0.615 0.120 -0.055 13.365 -7.832 -2.507 1 A_DC1:DG11B_B A 1 ? B 11 B 19 1 1 A DG 2 1_555 B DC 10 1_555 -1.153 -0.362 0.099 1.606 -8.762 -2.132 2 A_DG2:DC10B_B A 2 ? B 10 B 19 1 1 A DG 3 1_555 B DC 9 1_555 -1.075 -0.298 -0.036 1.319 -8.068 -2.385 3 A_DG3:DC9B_B A 3 ? B 9 B 19 1 1 A DT 4 1_555 B DA 8 1_555 0.539 -0.083 -0.226 3.498 -11.641 -3.905 4 A_DT4:DA8B_B A 4 ? B 8 B 20 1 1 A DC 5 1_555 B DG 7 1_555 1.089 -0.309 0.213 4.221 -11.809 -2.512 5 A_DC5:DG7B_B A 5 ? B 7 B 19 1 1 A DA 6 1_555 B DT 6 1_555 2.695 -4.852 -0.849 29.362 14.984 103.870 6 A_DA6:DT6B_B A 6 ? B 6 B ? ? 1 A DC 7 1_555 B DG 5 1_555 -0.306 0.139 0.645 -23.971 -0.161 -1.004 7 A_DC7:DG5B_B A 7 ? B 5 B 19 1 1 A DG 8 1_555 B DC 4 1_555 0.336 0.093 0.105 -1.535 -5.155 -1.148 8 A_DG8:DC4B_B A 8 ? B 4 B 19 1 1 A DA 9 1_555 B DT 3 1_555 -0.635 -0.115 0.077 1.342 -7.591 -2.565 9 A_DA9:DT3B_B A 9 ? B 3 B 20 1 1 A DG 10 1_555 B DC 2 1_555 -1.097 -0.315 -0.032 3.502 -5.225 -2.141 10 A_DG10:DC2B_B A 10 ? B 2 B 19 1 1 A DG 11 1_555 B DC 1 1_555 0.474 0.089 -0.289 -2.061 -4.328 -2.217 11 A_DG11:DC1B_B A 11 ? B 1 B 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 11 1_555 A DG 2 1_555 B DC 10 1_555 0.143 -1.492 3.274 -3.453 6.263 31.887 -3.692 -0.826 2.905 11.224 6.189 32.659 1 AA_DC1DG2:DC10BDG11B_BB A 1 ? B 11 B A 2 ? B 10 B 1 A DG 2 1_555 B DC 10 1_555 A DG 3 1_555 B DC 9 1_555 -0.109 -1.282 3.111 0.140 1.445 35.077 -2.329 0.201 3.057 2.397 -0.233 35.106 2 AA_DG2DG3:DC9BDC10B_BB A 2 ? B 10 B A 3 ? B 9 B 1 A DG 3 1_555 B DC 9 1_555 A DT 4 1_555 B DA 8 1_555 -0.331 -0.728 3.099 1.199 1.332 39.569 -1.222 0.620 3.063 1.967 -1.769 39.608 3 AA_DG3DT4:DA8BDC9B_BB A 3 ? B 9 B A 4 ? B 8 B 1 A DT 4 1_555 B DA 8 1_555 A DC 5 1_555 B DG 7 1_555 -0.112 -1.000 3.153 -4.300 2.414 33.609 -2.081 -0.467 3.066 4.147 7.388 33.959 4 AA_DT4DC5:DG7BDA8B_BB A 4 ? B 8 B A 5 ? B 7 B 1 A DC 5 1_555 B DG 7 1_555 A DA 6 1_555 B DT 6 1_555 0.823 -3.625 2.306 -174.009 -0.564 87.916 -1.811 -1.118 1.018 -0.285 87.920 175.689 5 AA_DC5DA6:DT6BDG7B_BB A 5 ? B 7 B A 6 ? B 6 B 1 A DA 6 1_555 B DT 6 1_555 A DC 7 1_555 B DG 5 1_555 -0.987 -5.527 -1.957 135.443 -77.783 46.175 -2.981 0.213 0.957 -42.467 -73.947 158.121 6 AA_DA6DC7:DG5BDT6B_BB A 6 ? B 6 B A 7 ? B 5 B 1 A DC 7 1_555 B DG 5 1_555 A DG 8 1_555 B DC 4 1_555 -0.341 -1.411 2.503 6.025 3.782 26.516 -3.650 1.795 2.156 8.062 -12.845 27.437 7 AA_DC7DG8:DC4BDG5B_BB A 7 ? B 5 B A 8 ? B 4 B 1 A DG 8 1_555 B DC 4 1_555 A DA 9 1_555 B DT 3 1_555 0.237 -1.433 2.990 0.659 3.767 27.784 -3.745 -0.351 2.780 7.798 -1.364 28.041 8 AA_DG8DA9:DT3BDC4B_BB A 8 ? B 4 B A 9 ? B 3 B 1 A DA 9 1_555 B DT 3 1_555 A DG 10 1_555 B DC 2 1_555 0.194 -1.723 3.053 -0.404 1.855 29.573 -3.727 -0.458 2.939 3.630 0.790 29.632 9 AA_DA9DG10:DC2BDT3B_BB A 9 ? B 3 B A 10 ? B 2 B 1 A DG 10 1_555 B DC 2 1_555 A DG 11 1_555 B DC 1 1_555 -0.096 -1.304 3.345 1.299 1.698 38.055 -2.215 0.313 3.281 2.602 -1.991 38.113 10 AA_DG10DG11:DC1BDC2B_BB A 10 ? B 2 B A 11 ? B 1 B # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '7S,8R,9R-TRIHYDROXY-7,8,9,10-TETRAHYDRO BENZO[A]PYRENE' _pdbx_entity_nonpoly.comp_id BPA #