data_2LG3 # _entry.id 2LG3 # _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 2LG3 pdb_00002lg3 10.2210/pdb2lg3/pdb RCSB RCSB102349 ? ? BMRB 17791 ? ? WWPDB D_1000102349 ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 17791 BMRB unspecified . 2LG2 PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LG3 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-07-19 _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 'Huang, H.' 1 'Wang, H.' 2 'Kozekova, A.' 3 'Lloyd, R.S.' 4 'Rizzo, C.J.' 5 'Stone, M.P.' 6 # _citation.id primary _citation.title ;Ring-chain tautomerization of trans-4-hydroxynonenal derived (6S,8R,11S) gamma-hydroxy-1,N2-propano-deoxyguanosine adduct when placed opposite 2'-deoxythymidine in duplex ; _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, H.' 1 ? primary 'Wang, H.' 2 ? primary 'Kozekova, A.' 3 ? primary 'Lloyd, R.S.' 4 ? primary 'Rizzo, C.J.' 5 ? primary 'Stone, M.P.' 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 ;DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') ; 3663.392 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3') ; 3678.403 1 ? ? ? ? 3 non-polymer syn '(4S)-nonane-1,4-diol' 160.254 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)(DT)(DA)(DG)(DC)(DG)(DA)(DG)(DT)(DC)(DC)' GCTAGCGAGTCC A ? 2 polydeoxyribonucleotide no no '(DG)(DG)(DA)(DC)(DT)(DT)(DG)(DC)(DT)(DA)(DG)(DC)' GGACTTGCTAGC 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 DT n 1 4 DA n 1 5 DG n 1 6 DC n 1 7 DG n 1 8 DA n 1 9 DG n 1 10 DT n 1 11 DC n 1 12 DC n 2 1 DG n 2 2 DG n 2 3 DA n 2 4 DC n 2 5 DT n 2 6 DT n 2 7 DG n 2 8 DC n 2 9 DT n 2 10 DA n 2 11 DG n 2 12 DC n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2LG3 2LG3 1 ? ? ? 2 PDB 2LG3 2LG3 2 ? ? ? # 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 2LG3 A 1 ? 12 ? 2LG3 1 ? 12 ? 1 12 2 2 2LG3 B 1 ? 12 ? 2LG3 13 ? 24 ? 13 24 # 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 HND non-polymer . '(4S)-nonane-1,4-diol' ? 'C9 H20 O2' 160.254 # _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.solution_id 1 _pdbx_nmr_exptl.type '2D 1H-1H NOESY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 100 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.contents ;1 mM DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'), 1 mM DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3'), 1 mM (2E,4R)-4-HYDROXYNON-2-ENAL, 100% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2LG3 _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 'back calculated data agree with experimental NOESY spectrum' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LG3 _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 2LG3 _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_software.authors 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name Amber _pdbx_nmr_software.version ? _pdbx_nmr_software.ordinal 1 # _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 2LG3 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LG3 _struct.title 'Structure of the duplex containing HNE derived (6S,8R,11S) gamma-HO-PdG when placed opposite dT' _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LG3 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'trans-4-hydroxynonenal, gamma-HO-PdG, 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 one ? A DG 7 N1 ? ? ? 1_555 C HND . C1 ? ? A DG 7 A HND 25 1_555 ? ? ? ? ? ? ? 1.484 ? ? covale2 covale one ? A DG 7 N2 ? ? ? 1_555 C HND . C3 ? ? A DG 7 A HND 25 1_555 ? ? ? ? ? ? ? 1.462 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 2 B DG 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 3 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 5 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 5 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 5 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 5 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 9 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 12 B DG 13 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 HND _struct_site.pdbx_auth_seq_id 25 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE HND A 25' # 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 5 DG A 7 ? DG A 7 . ? 1_555 ? 2 AC1 5 DA A 8 ? DA A 8 . ? 1_555 ? 3 AC1 5 DT B 5 ? DT B 17 . ? 1_555 ? 4 AC1 5 DT B 6 ? DT B 18 . ? 1_555 ? 5 AC1 5 DG B 7 ? DG B 19 . ? 1_555 ? # _atom_sites.entry_id 2LG3 _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 DG A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DC 12 12 12 DC DC A . n B 2 1 DG 1 13 13 DG DG B . n B 2 2 DG 2 14 14 DG DG B . n B 2 3 DA 3 15 15 DA DA B . n B 2 4 DC 4 16 16 DC DC B . n B 2 5 DT 5 17 17 DT DT B . n B 2 6 DT 6 18 18 DT DT B . n B 2 7 DG 7 19 19 DG DG B . n B 2 8 DC 8 20 20 DC DC B . n B 2 9 DT 9 21 21 DT DT B . n B 2 10 DA 10 22 22 DA DA B . n B 2 11 DG 11 23 23 DG DG B . n B 2 12 DC 12 24 24 DC DC B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id HND _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 25 _pdbx_nonpoly_scheme.auth_seq_num 25 _pdbx_nonpoly_scheme.pdb_mon_id HND _pdbx_nonpoly_scheme.auth_mon_id HNE _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 2012-08-01 2 'Structure model' 1 1 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 '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' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_software 4 2 'Structure model' pdbx_nmr_spectrometer 5 2 'Structure model' struct_conn 6 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_software.name' 5 2 'Structure model' '_pdbx_nmr_spectrometer.model' 6 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 2 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 2 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 2 'Structure model' '_struct_site.pdbx_auth_seq_id' # 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(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3')-1 ; 1 ? mM ? 1 ;DNA (5'-D(*GP*GP*AP*CP*TP*TP*GP*CP*TP*AP*GP*C)-3')-2 ; 1 ? mM ? 1 '(2E,4R)-4-HYDROXYNON-2-ENAL-3' 1 ? mM ? 1 # 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 N3 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 117.55 121.90 -4.35 0.70 N 2 1 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.40 117.00 -3.60 0.50 N 3 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 121.47 117.70 3.77 0.50 N 4 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 113.57 118.60 -5.03 0.60 N 5 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 110.18 108.30 1.88 0.30 N 6 1 N3 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 117.25 121.90 -4.65 0.70 N 7 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.35 108.30 2.05 0.30 N 8 1 N3 A DG 7 ? ? C2 A DG 7 ? ? N2 A DG 7 ? ? 113.71 119.90 -6.19 0.70 N 9 1 C4 A DA 8 ? ? C5 A DA 8 ? ? C6 A DA 8 ? ? 113.70 117.00 -3.30 0.50 N 10 1 C5 A DA 8 ? ? C6 A DA 8 ? ? N1 A DA 8 ? ? 121.33 117.70 3.63 0.50 N 11 1 N1 A DA 8 ? ? C6 A DA 8 ? ? N6 A DA 8 ? ? 113.52 118.60 -5.08 0.60 N 12 1 N3 A DC 11 ? ? C2 A DC 11 ? ? O2 A DC 11 ? ? 117.04 121.90 -4.86 0.70 N 13 1 N3 A DC 12 ? ? C2 A DC 12 ? ? O2 A DC 12 ? ? 117.55 121.90 -4.35 0.70 N 14 1 C4 B DA 15 ? ? C5 B DA 15 ? ? C6 B DA 15 ? ? 113.42 117.00 -3.58 0.50 N 15 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 121.28 117.70 3.58 0.50 N 16 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 113.69 118.60 -4.91 0.60 N 17 1 N3 B DC 16 ? ? C2 B DC 16 ? ? O2 B DC 16 ? ? 117.20 121.90 -4.70 0.70 N 18 1 C6 B DT 17 ? ? C5 B DT 17 ? ? C7 B DT 17 ? ? 119.22 122.90 -3.68 0.60 N 19 1 "O4'" B DT 18 ? ? "C4'" B DT 18 ? ? "C3'" B DT 18 ? ? 109.73 106.00 3.73 0.60 N 20 1 N3 B DT 18 ? ? C2 B DT 18 ? ? O2 B DT 18 ? ? 118.46 122.30 -3.84 0.60 N 21 1 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 118.62 122.90 -4.28 0.60 N 22 1 "O4'" B DG 19 ? ? "C4'" B DG 19 ? ? "C3'" B DG 19 ? ? 110.56 106.00 4.56 0.60 N 23 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 111.04 108.30 2.74 0.30 N 24 1 N3 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 117.43 121.90 -4.47 0.70 N 25 1 "O4'" B DT 21 ? ? "C1'" B DT 21 ? ? N1 B DT 21 ? ? 110.31 108.30 2.01 0.30 N 26 1 C6 B DT 21 ? ? C5 B DT 21 ? ? C7 B DT 21 ? ? 119.16 122.90 -3.74 0.60 N 27 1 C4 B DA 22 ? ? C5 B DA 22 ? ? C6 B DA 22 ? ? 113.75 117.00 -3.25 0.50 N 28 1 C5 B DA 22 ? ? C6 B DA 22 ? ? N1 B DA 22 ? ? 121.72 117.70 4.02 0.50 N 29 1 N1 B DA 22 ? ? C6 B DA 22 ? ? N6 B DA 22 ? ? 113.85 118.60 -4.75 0.60 N 30 1 "O4'" B DG 23 ? ? "C1'" B DG 23 ? ? N9 B DG 23 ? ? 111.13 108.30 2.83 0.30 N 31 1 N1 B DG 23 ? ? C6 B DG 23 ? ? O6 B DG 23 ? ? 116.23 119.90 -3.67 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 DG A 1 ? ? 0.067 'SIDE CHAIN' 2 1 DC A 6 ? ? 0.071 'SIDE CHAIN' 3 1 DG B 13 ? ? 0.073 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LG3 'double helix' 2LG3 'b-form double helix' 2LG3 '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 DG 1 1_555 B DC 12 1_555 -0.430 -0.109 0.288 9.416 13.724 2.814 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DC 2 1_555 B DG 11 1_555 0.223 -0.094 0.067 11.172 -11.081 -2.435 2 A_DC2:DG23_B A 2 ? B 23 ? 19 1 1 A DT 3 1_555 B DA 10 1_555 -0.181 0.074 -0.346 15.022 -10.785 -4.452 3 A_DT3:DA22_B A 3 ? B 22 ? 20 1 1 A DA 4 1_555 B DT 9 1_555 -0.010 -0.012 -0.065 -1.996 -16.240 -0.300 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DG 5 1_555 B DC 8 1_555 -0.167 -0.073 0.061 -5.409 -4.248 -1.299 5 A_DG5:DC20_B A 5 ? B 20 ? 19 1 1 A DC 6 1_555 B DG 7 1_555 0.392 -0.128 0.351 -8.360 -11.174 -0.758 6 A_DC6:DG19_B A 6 ? B 19 ? 19 1 1 A DA 8 1_555 B DT 5 1_555 0.108 0.038 -0.027 -10.157 12.022 -0.048 7 A_DA8:DT17_B A 8 ? B 17 ? 20 1 1 A DG 9 1_555 B DC 4 1_555 -0.367 -0.103 0.464 6.922 -0.876 -0.906 8 A_DG9:DC16_B A 9 ? B 16 ? 19 1 1 A DT 10 1_555 B DA 3 1_555 -0.206 -0.002 -0.067 3.780 -14.731 -0.506 9 A_DT10:DA15_B A 10 ? B 15 ? 20 1 1 A DC 11 1_555 B DG 2 1_555 0.336 -0.117 -0.062 -3.561 -6.496 -0.381 10 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DC 12 1_555 B DG 1 1_555 0.457 -0.134 0.428 -13.920 3.963 0.255 11 A_DC12:DG13_B A 12 ? B 13 ? 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 DG 1 1_555 B DC 12 1_555 A DC 2 1_555 B DG 11 1_555 -0.472 -0.599 3.359 1.586 4.776 31.766 -1.945 1.140 3.210 8.657 -2.876 32.152 1 AA_DG1DC2:DG23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DC 2 1_555 B DG 11 1_555 A DT 3 1_555 B DA 10 1_555 -0.052 -0.938 3.272 2.196 1.373 29.163 -2.152 0.574 3.213 2.721 -4.350 29.276 2 AA_DC2DT3:DA22DG23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DT 3 1_555 B DA 10 1_555 A DA 4 1_555 B DT 9 1_555 0.313 -1.025 3.618 -1.291 19.370 32.470 -4.170 -0.657 2.608 31.390 2.093 37.696 3 AA_DT3DA4:DT21DA22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B DT 9 1_555 A DG 5 1_555 B DC 8 1_555 -0.215 -1.105 3.430 -1.556 -0.604 31.976 -1.888 0.095 3.456 -1.095 2.821 32.018 4 AA_DA4DG5:DC20DT21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DG 5 1_555 B DC 8 1_555 A DC 6 1_555 B DG 7 1_555 -0.246 -0.960 3.418 -3.545 5.165 38.442 -2.085 -0.073 3.276 7.781 5.341 38.931 5 AA_DG5DC6:DG19DC20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 8 1_555 B DT 5 1_555 A DG 9 1_555 B DC 4 1_555 0.832 -1.319 3.122 -1.280 -7.674 21.411 -0.536 -2.577 3.332 -19.831 3.308 22.765 6 AA_DA8DG9:DC16DT17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DG 9 1_555 B DC 4 1_555 A DT 10 1_555 B DA 3 1_555 -0.420 -1.016 3.466 5.553 0.906 36.842 -1.716 1.429 3.344 1.423 -8.723 37.255 7 AA_DG9DT10:DA15DC16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DT 10 1_555 B DA 3 1_555 A DC 11 1_555 B DG 2 1_555 0.085 -0.340 3.459 -1.197 1.824 40.900 -0.696 -0.260 3.437 2.608 1.712 40.956 8 AA_DT10DC11:DG14DA15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DC 12 1_555 B DG 1 1_555 -0.086 -0.726 3.668 -5.394 -0.196 38.519 -1.065 -0.607 3.650 -0.295 8.128 38.882 9 AA_DC11DC12:DG13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name '(4S)-nonane-1,4-diol' _pdbx_entity_nonpoly.comp_id HND #