data_140D # _entry.id 140D # _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 140D pdb_0000140d 10.2210/pdb140d/pdb WWPDB D_1000170094 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 141D '1 STRUCTURE (B DNA USED AS STARTING STRUCTURE)' unspecified PDB 142D 'MINIMIZED AVERAGE STRUCTURE' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 140D _pdbx_database_status.recvd_initial_deposition_date 1993-09-24 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _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 'Mujeeb, A.' 1 'Kerwin, S.M.' 2 'Kenyon, G.L.' 3 'James, T.L.' 4 # _citation.id primary _citation.title ;Solution structure of a conserved DNA sequence from the HIV-1 genome: restrained molecular dynamics simulation with distance and torsion angle restraints derived from two-dimensional NMR spectra. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 32 _citation.page_first 13419 _citation.page_last 13431 _citation.year 1993 _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 8257678 _citation.pdbx_database_id_DOI 10.1021/bi00212a007 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Mujeeb, A.' 1 ? primary 'Kerwin, S.M.' 2 ? primary 'Kenyon, G.L.' 3 ? primary 'James, T.L.' 4 ? # _cell.entry_id 140D _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 140D _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(*AP*GP*CP*TP*TP*GP*CP*CP*TP*TP*GP*AP*G)-3') ; 3982.596 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*TP*CP*AP*AP*GP*GP*CP*AP*AP*GP*CP*T)-3') ; 3960.600 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 '(DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC)(DT)(DT)(DG)(DA)(DG)' AGCTTGCCTTGAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DC)(DA)(DA)(DG)(DG)(DC)(DA)(DA)(DG)(DC)(DT)' CTCAAGGCAAGCT B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DG n 1 3 DC n 1 4 DT n 1 5 DT n 1 6 DG n 1 7 DC n 1 8 DC n 1 9 DT n 1 10 DT n 1 11 DG n 1 12 DA n 1 13 DG n 2 1 DC n 2 2 DT n 2 3 DC n 2 4 DA n 2 5 DA n 2 6 DG n 2 7 DG n 2 8 DC n 2 9 DA n 2 10 DA n 2 11 DG n 2 12 DC n 2 13 DT n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'CHEMICALLY SYNTHESIZED' 2 1 sample ? ? ? ? ? 'CHEMICALLY SYNTHESIZED' # 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 140D 140D ? ? ? 2 2 PDB 140D 140D ? ? ? # 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 140D A 1 ? 13 ? 140D 1 ? 13 ? 1 13 2 2 140D B 1 ? 13 ? 140D 14 ? 26 ? 14 26 # 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 # _pdbx_nmr_refine.entry_id 140D _pdbx_nmr_refine.method 'MOLECULAR DYNAMICS, ENERGY MINIMIZATION' _pdbx_nmr_refine.details ;ALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED THREE COORDINATE SETS FOR THIS STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN DATA BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA AND B-DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE AUTHORS DENOTED THESE STRUCTURES AS RMD-A AND RMD-B, RESPECTIVELY. THE THIRD COORDINATE SET (PROTEIN DATA BANK ENTRY 142D) REPRESENTS THE FINAL STRUCTURE, DENOTED RMD-FINAL BY THE AUTHORS. ALL STRUCTURES WERE DERIVED BY AVERAGING THE LAST 4 PS OF 30 PS RESTRAINED MD (AMBER4) AND SUBSEQUENT RESTRAINED ENERGY MINIMIZATION. FIVE RMD RUNS WERE AVERAGED TO EACH INTERIM STRUCTURE RMD-A AND RMD-B, DEPENDING ON THE STARTING GEOMETRY. ALL TEN STRUCTURES WERE AVERAGED, RESTRAINED ENERGY MINIMIZED AND A FINAL 20PS RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, AFTER AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE FINAL STRUCTURE: RMD-FINAL. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 140D _pdbx_nmr_details.text ;SUGAR PUCKER OF DEOXYRIBOSES HAS BEEN DETERMINED BY SIMULATION OF 2QF-COSY SPECTRA. A LIST OF TORSION ANGLE AND NOE DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRY R140DMR. ; # _pdbx_nmr_ensemble.entry_id 140D _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal AMBER4 ? 'structure solution' ? 1 AMBER4 ? refinement ? 2 # _exptl.entry_id 140D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 140D _struct.title ;SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 140D _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, DOUBLE HELIX, CONSERVED SEQUENCE OF HIV-1 GENOME' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_biol.id 1 _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 hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B DT 13 N3 ? ? A DA 1 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B DT 13 O4 ? ? A DA 1 B DT 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 2 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 2 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 2 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 3 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 3 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 3 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 4 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 10 N6 ? ? A DT 4 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 9 N1 ? ? A DT 5 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 9 N6 ? ? A DT 5 B DA 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 6 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 6 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 6 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 7 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 7 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 7 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 8 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 8 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 8 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 9 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 9 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 10 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 10 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 11 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 12 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 12 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 140D _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 140D _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 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 DA 1 1 1 DA A A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DC 3 3 3 DC C A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DG 6 6 6 DG G A . n A 1 7 DC 7 7 7 DC C A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DT 10 10 10 DT T A . n A 1 11 DG 11 11 11 DG G A . n A 1 12 DA 12 12 12 DA A A . n A 1 13 DG 13 13 13 DG G A . n B 2 1 DC 1 14 14 DC C B . n B 2 2 DT 2 15 15 DT T B . n B 2 3 DC 3 16 16 DC C B . n B 2 4 DA 4 17 17 DA A B . n B 2 5 DA 5 18 18 DA A B . n B 2 6 DG 6 19 19 DG G B . n B 2 7 DG 7 20 20 DG G B . n B 2 8 DC 8 21 21 DC C B . n B 2 9 DA 9 22 22 DA A B . n B 2 10 DA 10 23 23 DA A B . n B 2 11 DG 11 24 24 DG G B . n B 2 12 DC 12 25 25 DC C B . n B 2 13 DT 13 26 26 DT T B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 1994-04-30 2 'Structure model' 1 1 2008-03-03 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 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 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' # _software.name AMBER _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 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 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 113.44 108.30 5.14 0.30 N 2 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 114.15 108.30 5.85 0.30 N 3 1 "O4'" A DT 4 ? ? "C4'" A DT 4 ? ? "C3'" A DT 4 ? ? 109.63 106.00 3.63 0.60 N 4 1 "C5'" A DT 4 ? ? "C4'" A DT 4 ? ? "O4'" A DT 4 ? ? 117.14 109.80 7.34 1.10 N 5 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 110.85 108.30 2.55 0.30 N 6 1 "O4'" A DT 5 ? ? "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? 110.21 106.00 4.21 0.60 N 7 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 114.28 108.30 5.98 0.30 N 8 1 "O4'" A DC 8 ? ? "C1'" A DC 8 ? ? N1 A DC 8 ? ? 110.57 108.30 2.27 0.30 N 9 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 112.22 108.30 3.92 0.30 N 10 1 "O4'" A DT 10 ? ? "C1'" A DT 10 ? ? N1 A DT 10 ? ? 110.59 108.30 2.29 0.30 N 11 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 114.09 108.30 5.79 0.30 N 12 1 "O4'" A DA 12 ? ? "C4'" A DA 12 ? ? "C3'" A DA 12 ? ? 111.14 106.00 5.14 0.60 N 13 1 "O4'" A DG 13 ? ? "C1'" A DG 13 ? ? N9 A DG 13 ? ? 113.40 108.30 5.10 0.30 N 14 1 "O4'" B DC 14 ? ? "C1'" B DC 14 ? ? N1 B DC 14 ? ? 110.54 108.30 2.24 0.30 N 15 1 "O4'" B DT 15 ? ? "C1'" B DT 15 ? ? N1 B DT 15 ? ? 111.42 108.30 3.12 0.30 N 16 1 "O4'" B DC 16 ? ? "C4'" B DC 16 ? ? "C3'" B DC 16 ? ? 112.75 106.00 6.75 0.60 N 17 1 "C5'" B DC 16 ? ? "C4'" B DC 16 ? ? "O4'" B DC 16 ? ? 118.55 109.80 8.75 1.10 N 18 1 "C3'" B DC 16 ? ? "C2'" B DC 16 ? ? "C1'" B DC 16 ? ? 110.74 102.50 8.24 1.20 N 19 1 "O4'" B DC 16 ? ? "C1'" B DC 16 ? ? N1 B DC 16 ? ? 111.93 108.30 3.63 0.30 N 20 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 114.05 108.30 5.75 0.30 N 21 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? N9 B DA 18 ? ? 112.99 108.30 4.69 0.30 N 22 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 112.81 108.30 4.51 0.30 N 23 1 "O4'" B DG 20 ? ? "C4'" B DG 20 ? ? "C3'" B DG 20 ? ? 111.25 106.00 5.25 0.60 N 24 1 "O4'" B DC 21 ? ? "C4'" B DC 21 ? ? "C3'" B DC 21 ? ? 110.35 106.00 4.35 0.60 N 25 1 "C5'" B DC 21 ? ? "C4'" B DC 21 ? ? "O4'" B DC 21 ? ? 116.76 109.80 6.96 1.10 N 26 1 "O4'" B DA 22 ? ? "C1'" B DA 22 ? ? N9 B DA 22 ? ? 112.43 108.30 4.13 0.30 N 27 1 "O4'" B DA 23 ? ? "C1'" B DA 23 ? ? N9 B DA 23 ? ? 110.18 108.30 1.88 0.30 N 28 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 113.05 108.30 4.75 0.30 N 29 1 "O4'" B DC 25 ? ? "C4'" B DC 25 ? ? "C3'" B DC 25 ? ? 109.66 106.00 3.66 0.60 N 30 1 "O4'" B DC 25 ? ? "C1'" B DC 25 ? ? N1 B DC 25 ? ? 110.29 108.30 1.99 0.30 N 31 1 "O4'" B DT 26 ? ? "C1'" B DT 26 ? ? N1 B DT 26 ? ? 111.58 108.30 3.28 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 DC A 3 ? ? 0.086 'SIDE CHAIN' 2 1 DG A 6 ? ? 0.071 'SIDE CHAIN' 3 1 DC A 7 ? ? 0.085 'SIDE CHAIN' 4 1 DG A 11 ? ? 0.067 'SIDE CHAIN' 5 1 DC B 16 ? ? 0.081 'SIDE CHAIN' 6 1 DA B 17 ? ? 0.068 'SIDE CHAIN' 7 1 DA B 18 ? ? 0.063 'SIDE CHAIN' 8 1 DC B 21 ? ? 0.069 'SIDE CHAIN' 9 1 DG B 24 ? ? 0.092 'SIDE CHAIN' 10 1 DC B 25 ? ? 0.068 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 140D 'double helix' 140D '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 DA 1 1_555 B DT 13 1_555 0.204 -0.100 -0.062 -6.836 -13.781 -5.661 1 A_DA1:DT26_B A 1 ? B 26 ? 20 1 1 A DG 2 1_555 B DC 12 1_555 -0.321 -0.178 0.451 3.453 -10.858 0.029 2 A_DG2:DC25_B A 2 ? B 25 ? 19 1 1 A DC 3 1_555 B DG 11 1_555 0.064 -0.171 0.343 -10.412 -14.471 -3.284 3 A_DC3:DG24_B A 3 ? B 24 ? 19 1 1 A DT 4 1_555 B DA 10 1_555 0.018 -0.166 0.174 -6.435 -10.834 0.084 4 A_DT4:DA23_B A 4 ? B 23 ? 20 1 1 A DT 5 1_555 B DA 9 1_555 -0.043 -0.116 0.027 8.000 -3.940 -2.714 5 A_DT5:DA22_B A 5 ? B 22 ? 20 1 1 A DG 6 1_555 B DC 8 1_555 -0.458 -0.228 0.293 9.641 -13.446 -0.370 6 A_DG6:DC21_B A 6 ? B 21 ? 19 1 1 A DC 7 1_555 B DG 7 1_555 0.202 -0.158 0.658 -12.606 10.584 1.413 7 A_DC7:DG20_B A 7 ? B 20 ? 19 1 1 A DC 8 1_555 B DG 6 1_555 0.471 -0.238 0.440 -5.175 -3.866 -0.358 8 A_DC8:DG19_B A 8 ? B 19 ? 19 1 1 A DT 9 1_555 B DA 5 1_555 -0.227 -0.096 -0.035 -9.284 -15.844 -4.437 9 A_DT9:DA18_B A 9 ? B 18 ? 20 1 1 A DT 10 1_555 B DA 4 1_555 -0.054 -0.138 -0.122 1.459 -1.689 1.478 10 A_DT10:DA17_B A 10 ? B 17 ? 20 1 1 A DG 11 1_555 B DC 3 1_555 -0.423 -0.264 -0.322 2.391 -9.655 -1.202 11 A_DG11:DC16_B A 11 ? B 16 ? 19 1 1 A DA 12 1_555 B DT 2 1_555 -0.018 -0.109 -0.319 -10.687 -1.074 3.462 12 A_DA12:DT15_B A 12 ? B 15 ? 20 1 1 A DG 13 1_555 B DC 1 1_555 -0.278 -0.203 0.243 0.547 -3.618 -2.556 13 A_DG13:DC14_B A 13 ? B 14 ? 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 DA 1 1_555 B DT 13 1_555 A DG 2 1_555 B DC 12 1_555 0.493 -0.551 2.898 -2.580 -4.554 30.772 -0.251 -1.355 2.897 -8.504 4.818 31.203 1 AA_DA1DG2:DC25DT26_BB A 1 ? B 26 ? A 2 ? B 25 ? 1 A DG 2 1_555 B DC 12 1_555 A DC 3 1_555 B DG 11 1_555 0.092 -0.996 3.448 2.344 3.666 38.174 -1.990 0.164 3.341 5.583 -3.570 38.412 2 AA_DG2DC3:DG24DC25_BB A 2 ? B 25 ? A 3 ? B 24 ? 1 A DC 3 1_555 B DG 11 1_555 A DT 4 1_555 B DA 10 1_555 0.631 -0.504 3.138 4.032 -0.666 34.655 -0.742 -0.458 3.198 -1.114 -6.739 34.888 3 AA_DC3DT4:DA23DG24_BB A 3 ? B 24 ? A 4 ? B 23 ? 1 A DT 4 1_555 B DA 10 1_555 A DT 5 1_555 B DA 9 1_555 -0.081 -0.413 3.069 -1.184 -2.117 32.873 -0.388 -0.048 3.090 -3.735 2.089 32.960 4 AA_DT4DT5:DA22DA23_BB A 4 ? B 23 ? A 5 ? B 22 ? 1 A DT 5 1_555 B DA 9 1_555 A DG 6 1_555 B DC 8 1_555 0.205 -0.690 3.025 -2.784 5.967 29.082 -2.464 -0.922 2.800 11.694 5.455 29.803 5 AA_DT5DG6:DC21DA22_BB A 5 ? B 22 ? A 6 ? B 21 ? 1 A DG 6 1_555 B DC 8 1_555 A DC 7 1_555 B DG 7 1_555 -0.203 -0.641 4.058 -2.050 21.751 37.332 -3.459 0.033 3.236 30.954 2.918 43.058 6 AA_DG6DC7:DG20DC21_BB A 6 ? B 21 ? A 7 ? B 20 ? 1 A DC 7 1_555 B DG 7 1_555 A DC 8 1_555 B DG 6 1_555 0.104 -0.197 3.162 1.639 9.685 33.233 -1.764 0.068 2.991 16.491 -2.790 34.615 7 AA_DC7DC8:DG19DG20_BB A 7 ? B 20 ? A 8 ? B 19 ? 1 A DC 8 1_555 B DG 6 1_555 A DT 9 1_555 B DA 5 1_555 0.365 -0.435 3.120 7.740 8.276 33.419 -1.891 0.492 2.942 13.904 -13.004 35.236 8 AA_DC8DT9:DA18DG19_BB A 8 ? B 19 ? A 9 ? B 18 ? 1 A DT 9 1_555 B DA 5 1_555 A DT 10 1_555 B DA 4 1_555 1.290 0.190 3.006 1.090 0.928 37.427 0.184 -1.877 3.045 1.446 -1.698 37.453 9 AA_DT9DT10:DA17DA18_BB A 9 ? B 18 ? A 10 ? B 17 ? 1 A DT 10 1_555 B DA 4 1_555 A DG 11 1_555 B DC 3 1_555 -0.039 -0.263 3.080 1.487 15.733 26.987 -3.258 0.334 2.541 30.607 -2.892 31.199 10 AA_DT10DG11:DC16DA17_BB A 10 ? B 17 ? A 11 ? B 16 ? 1 A DG 11 1_555 B DC 3 1_555 A DA 12 1_555 B DT 2 1_555 -0.369 -1.705 3.356 -2.865 9.840 31.816 -4.529 0.187 2.744 17.394 5.065 33.385 11 AA_DG11DA12:DT15DC16_BB A 11 ? B 16 ? A 12 ? B 15 ? 1 A DA 12 1_555 B DT 2 1_555 A DG 13 1_555 B DC 1 1_555 -0.166 -0.790 2.905 -3.935 -2.452 33.673 -1.000 -0.283 2.953 -4.209 6.754 33.982 12 AA_DA12DG13:DC14DT15_BB A 12 ? B 15 ? A 13 ? B 14 ? #