data_2LZV # _entry.id 2LZV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 2LZV pdb_00002lzv 10.2210/pdb2lzv/pdb RCSB RCSB103031 ? ? BMRB 18780 ? ? WWPDB D_1000103031 ? ? # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 1N4B PDB . unspecified 1S37 PDB . unspecified 1XCI PDB . unspecified 2LZW PDB . unspecified 18780 BMRB . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LZV _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-10-11 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Denisov, A.Y.' 1 'McManus, F.P.' 2 'Noronha, A.M.' 3 'Wilds, C.J.' 4 # _citation.id primary _citation.title 'Structural basis of interstrand cross-link repair by O 6 -alkylguanine DNA alkyltransferase.' _citation.journal_abbrev Org.Biomol.Chem. _citation.journal_volume 15 _citation.page_first 8361 _citation.page_last 8370 _citation.year 2017 _citation.journal_id_ASTM ? _citation.country UK _citation.journal_id_ISSN 1477-0539 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 28937154 _citation.pdbx_database_id_DOI 10.1039/c7ob02093g # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Denisov, A.Y.' 1 ? primary 'McManus, F.P.' 2 ? primary ;O'Flaherty, D.K. ; 3 ? primary 'Noronha, A.M.' 4 ? primary 'Wilds, C.J.' 5 ? # 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*AP*AP*AP*UP*TP*TP*TP*CP*G)-3') ; 3334.183 2 ? ? ? ? 2 non-polymer syn HEPTANE 100.202 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DA)(DA)(DA)(DU)(DT)(DT)(DT)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGAAAUTTTCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # 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 DA n 1 4 DA n 1 5 DA n 1 6 DU n 1 7 DT n 1 8 DT n 1 9 DT n 1 10 DC n 1 11 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2LZV _struct_ref.pdbx_db_accession 2LZV _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 2LZV A 1 ? 11 ? 2LZV 1 ? 11 ? 1 11 2 1 2LZV B 1 ? 11 ? 2LZV 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 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 DU 'DNA linking' y "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O8 P' 308.182 HP6 non-polymer . HEPTANE ? 'C7 H16' 100.202 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 1 2 1 '2D TOCSY' 1 3 1 '2D DQF-COSY' 1 4 1 '2D 1H-31P HSQC' 2 5 2 '2D NOESY' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.temperature_units 1 0.1 7.5 ambient ? 298 K 2 0.1 7.5 ambient ? 273 K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;0.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), 100% D2O ; 1 '100% D2O' ;0.5 mM DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3'), 90% H2O/10% D2O ; 2 '90% H2O/10% D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 500 Varian 'Unity Inova' 1 'Varian Unity Inova' 800 Varian 'Unity Inova' 2 'Varian Unity Inova' 500 Varian VNMRS 3 'Varian VNMRS' # _pdbx_nmr_refine.entry_id 2LZV _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the least restraint violations and the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LZV _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2LZV _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Brunger, Adams, Clore, Gros, Nilges and Read' refinement CNS 1.2 1 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' processing NMRPipe ? 2 'Johnson, One Moon Scientific' 'data analysis' NMRView ? 3 Varian collection VnmrJ ? 4 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2LZV _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LZV _struct.title 'DNA duplex containing mispair-aligned O4U-heptylene-O4U interstrand cross-link' _struct.pdbx_model_details 'minimized average structure, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 2LZV _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'INTERSTRAND CROSS-LINK, 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 1 ? C 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 _struct_conn.pdbx_role covale1 covale none ? A DU 6 O4 ? ? ? 1_555 C HP6 . C20 ? ? A DU 6 B HP6 101 1_555 ? ? ? ? ? ? ? 1.430 ? ? covale2 covale none ? B DU 6 O4 ? ? ? 1_555 C HP6 . C26 ? ? B DU 6 B HP6 101 1_555 ? ? ? ? ? ? ? 1.429 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 3 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 3 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 4 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 4 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 5 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 5 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 7 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 7 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 8 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 8 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 9 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 9 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? 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 B _struct_site.pdbx_auth_comp_id HP6 _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE HP6 B 101' # 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 2 DU A 6 ? DU A 6 . ? 1_555 ? 2 AC1 2 DU B 6 ? DU B 6 . ? 1_555 ? # _atom_sites.entry_id 2LZV _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 DA 3 3 3 DA DA A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DU 6 6 6 DU DU A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DG 11 11 11 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DA 3 3 3 DA DA B . n B 1 4 DA 4 4 4 DA DA B . n B 1 5 DA 5 5 5 DA DA B . n B 1 6 DU 6 6 6 DU DU B . n B 1 7 DT 7 7 7 DT DT B . n B 1 8 DT 8 8 8 DT DT B . n B 1 9 DT 9 9 9 DT DT B . n B 1 10 DC 10 10 10 DC DC B . n B 1 11 DG 11 11 11 DG DG B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id HP6 _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 12 _pdbx_nonpoly_scheme.pdb_mon_id HP6 _pdbx_nonpoly_scheme.auth_mon_id HP6 _pdbx_nonpoly_scheme.pdb_strand_id B _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 2013-10-16 2 'Structure model' 1 1 2017-10-04 3 'Structure model' 1 2 2022-08-24 4 'Structure model' 1 3 2023-06-14 # _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' 'Source and taxonomy' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 3 'Structure model' 'Derived calculations' 6 4 '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 2 'Structure model' citation 2 2 'Structure model' pdbx_entity_src_syn 3 3 'Structure model' citation 4 3 'Structure model' database_2 5 3 'Structure model' pdbx_nmr_software 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site 8 4 'Structure model' pdbx_database_status # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.pdbx_database_id_DOI' 6 2 'Structure model' '_citation.pdbx_database_id_PubMed' 7 2 'Structure model' '_citation.title' 8 2 'Structure model' '_citation.year' 9 3 'Structure model' '_citation.journal_abbrev' 10 3 'Structure model' '_citation.journal_volume' 11 3 'Structure model' '_citation.page_first' 12 3 'Structure model' '_citation.page_last' 13 3 'Structure model' '_citation.title' 14 3 'Structure model' '_database_2.pdbx_DOI' 15 3 'Structure model' '_database_2.pdbx_database_accession' 16 3 'Structure model' '_pdbx_nmr_software.name' 17 3 'Structure model' '_struct_conn.pdbx_dist_value' 18 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 19 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 20 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 21 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 22 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 23 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 24 3 'Structure model' '_struct_site.pdbx_auth_seq_id' 25 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling _pdbx_nmr_exptl_sample.solution_id ;DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')-1 ; 0.5 ? mM ? 1 ;DNA (5'-D(*CP*GP*AP*AP*AP*UP*TP*TP*TP*CP*G)-3')-2 ; 0.5 ? mM ? 2 # 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 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.373 1.232 0.141 0.008 N 2 1 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 3 2 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.372 1.232 0.140 0.008 N 4 2 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 5 3 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.373 1.232 0.141 0.008 N 6 3 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 7 4 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.374 1.232 0.142 0.008 N 8 4 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 9 5 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.375 1.232 0.143 0.008 N 10 5 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.375 1.232 0.143 0.008 N 11 6 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.372 1.232 0.140 0.008 N 12 6 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.373 1.232 0.141 0.008 N 13 7 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.373 1.232 0.141 0.008 N 14 7 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.371 1.232 0.139 0.008 N 15 8 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.373 1.232 0.141 0.008 N 16 8 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 17 9 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.374 1.232 0.142 0.008 N 18 9 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 19 10 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.373 1.232 0.141 0.008 N 20 10 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.372 1.232 0.140 0.008 N 21 11 C4 A DU 6 ? ? O4 A DU 6 ? ? 1.373 1.232 0.141 0.008 N 22 11 C4 B DU 6 ? ? O4 B DU 6 ? ? 1.373 1.232 0.141 0.008 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LZV 'b-form double helix' 2LZV 'mismatched base pair' # 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 -0.480 -0.455 -1.124 7.521 17.724 -11.915 1 A_DC1:DG11_B A 1 ? B 11 ? 19 1 1 A DG 2 1_555 B DC 10 1_555 -0.117 -0.253 -0.595 -1.369 -5.625 3.618 2 A_DG2:DC10_B A 2 ? B 10 ? 19 1 1 A DA 3 1_555 B DT 9 1_555 -0.189 -0.264 -0.279 -1.331 -3.277 7.713 3 A_DA3:DT9_B A 3 ? B 9 ? 20 1 1 A DA 4 1_555 B DT 8 1_555 0.079 -0.300 -0.186 7.129 -3.478 3.253 4 A_DA4:DT8_B A 4 ? B 8 ? 20 1 1 A DA 5 1_555 B DT 7 1_555 -0.062 -0.145 0.006 15.164 -10.143 -6.125 5 A_DA5:DT7_B A 5 ? B 7 ? 20 1 1 A DT 7 1_555 B DA 5 1_555 0.066 -0.143 0.013 -15.103 -9.968 -6.254 6 A_DT7:DA5_B A 7 ? B 5 ? 20 1 1 A DT 8 1_555 B DA 4 1_555 -0.065 -0.300 -0.184 -7.118 -3.382 3.231 7 A_DT8:DA4_B A 8 ? B 4 ? 20 1 1 A DT 9 1_555 B DA 3 1_555 0.204 -0.272 -0.276 1.303 -3.174 7.490 8 A_DT9:DA3_B A 9 ? B 3 ? 20 1 1 A DC 10 1_555 B DG 2 1_555 0.127 -0.266 -0.581 1.486 -5.664 3.567 9 A_DC10:DG2_B A 10 ? B 2 ? 19 1 1 A DG 11 1_555 B DC 1 1_555 0.481 -0.470 -1.104 -7.103 17.822 -11.829 10 A_DG11:DC1_B A 11 ? B 1 ? 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 0.956 -0.485 4.121 -2.056 25.930 25.452 -5.181 -1.885 2.524 46.211 3.664 36.238 1 AA_DC1DG2:DC10DG11_BB A 1 ? B 11 ? A 2 ? B 10 ? 1 A DG 2 1_555 B DC 10 1_555 A DA 3 1_555 B DT 9 1_555 0.303 -0.479 3.009 -3.052 12.290 33.616 -2.353 -0.884 2.642 20.374 5.060 35.858 2 AA_DG2DA3:DT9DC10_BB A 2 ? B 10 ? A 3 ? B 9 ? 1 A DA 3 1_555 B DT 9 1_555 A DA 4 1_555 B DT 8 1_555 -0.541 -0.395 2.975 -1.031 11.865 31.685 -2.394 0.782 2.675 20.833 1.809 33.795 3 AA_DA3DA4:DT8DT9_BB A 3 ? B 9 ? A 4 ? B 8 ? 1 A DA 4 1_555 B DT 8 1_555 A DA 5 1_555 B DT 7 1_555 -1.286 0.222 2.949 -2.206 6.296 36.954 -0.410 1.733 3.014 9.834 3.445 37.530 4 AA_DA4DA5:DT7DT8_BB A 4 ? B 8 ? A 5 ? B 7 ? 1 A DT 7 1_555 B DA 5 1_555 A DT 8 1_555 B DA 4 1_555 1.289 0.218 2.950 2.271 6.314 37.021 -0.418 -1.729 3.016 9.845 -3.540 37.603 5 AA_DT7DT8:DA4DA5_BB A 7 ? B 5 ? A 8 ? B 4 ? 1 A DT 8 1_555 B DA 4 1_555 A DT 9 1_555 B DA 3 1_555 0.536 -0.397 2.977 1.070 11.861 31.685 -2.398 -0.768 2.676 20.826 -1.879 33.795 6 AA_DT8DT9:DA3DA4_BB A 8 ? B 4 ? A 9 ? B 3 ? 1 A DT 9 1_555 B DA 3 1_555 A DC 10 1_555 B DG 2 1_555 -0.298 -0.484 3.009 3.020 12.147 33.613 -2.349 0.874 2.646 20.157 -5.012 35.805 7 AA_DT9DC10:DG2DA3_BB A 9 ? B 3 ? A 10 ? B 2 ? 1 A DC 10 1_555 B DG 2 1_555 A DG 11 1_555 B DC 1 1_555 -0.949 -0.491 4.111 2.105 25.922 25.511 -5.164 1.880 2.517 46.135 -3.746 36.276 8 AA_DC10DG11:DC1DG2_BB A 10 ? B 2 ? A 11 ? B 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name HEPTANE _pdbx_entity_nonpoly.comp_id HP6 #