data_1DK9 # _entry.id 1DK9 # _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 1DK9 pdb_00001dk9 10.2210/pdb1dk9/pdb RCSB RCSB010154 ? ? WWPDB D_1000010154 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1DK6 _pdbx_database_related.details 'Residue 14 is replaced by 3-nitropyrrole' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DK9 _pdbx_database_status.recvd_initial_deposition_date 1999-12-06 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Klewer, D.A.' 1 'Hoskins, A.' 2 'Davisson, V.J.' 3 'Bergstrom, D.E.' 4 'LiWang, A.C.' 5 # _citation.id primary _citation.title ;NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control. ; _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 28 _citation.page_first 4514 _citation.page_last 4522 _citation.year 2000 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 11071940 _citation.pdbx_database_id_DOI 10.1093/nar/28.22.4514 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Klewer, D.A.' 1 ? primary 'Hoskins, A.' 2 ? primary 'Zhang, P.' 3 ? primary 'Davisson, V.J.' 4 ? primary 'Bergstrom, D.E.' 5 ? primary 'LiWang, A.C.' 6 ? # _cell.entry_id 1DK9 _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 1DK9 _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 "5'-D(CP*AP*TP*GP*AP*GP*TP*AP*CP*)-3'" 2739.824 1 ? ? ? ? 2 polymer syn "5'-D(GP*TP*AP*CP*TP*CP*AP*TP*GP*)-3'" 2730.810 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)(DA)(DT)(DG)(DA)(DG)(DT)(DA)(DC)' CATGAGTAC A ? 2 polydeoxyribonucleotide no no '(DG)(DT)(DA)(DC)(DT)(DC)(DA)(DT)(DG)' GTACTCATG 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 DA n 1 3 DT n 1 4 DG n 1 5 DA n 1 6 DG n 1 7 DT n 1 8 DA n 1 9 DC n 2 1 DG n 2 2 DT n 2 3 DA n 2 4 DC n 2 5 DT n 2 6 DC n 2 7 DA n 2 8 DT n 2 9 DG 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 ? ? ? ? ? 'THIS SEQUENCE WAS CHEMICALLY SYNTHESIZED' 2 1 sample ? ? ? ? ? 'THIS SEQUENCE WAS 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 1DK9 1DK9 ? ? ? 2 2 PDB 1DK9 1DK9 ? ? ? # 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 1DK9 A 1 ? 9 ? 1DK9 1 ? 9 ? 1 9 2 2 1DK9 B 1 ? 9 ? 1DK9 10 ? 18 ? 10 18 # 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 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 DQF-COSY # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _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 '4.5mM duplex, 100mM NaCl, 10mM NaOP, 1mM EDTA' _pdbx_nmr_sample_details.solvent_system '95% H2O/5% D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Varian _pdbx_nmr_spectrometer.model INOVA _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_ensemble.entry_id 1DK9 _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 CORMA 5.2 'iterative matrix relaxation' Liu 1 MARDIGRAS 5.2 'iterative matrix relaxation' 'Borgias, James' 2 NMRPipe 7.1 processing Delaglio 3 VNMR 6.1B collection Varian 4 X-PLOR V3.840 refinement Brunger 5 PIPP 4.2.7 'data analysis' Garrett 6 # _exptl.entry_id 1DK9 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1DK9 _struct.title 'SOLUTION STRUCTURE ANALYSIS OF THE DNA DUPLEX D(CATGAGTAC)D(GTACTCATG)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DK9 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, DUPLEX' # 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 # 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 DC 1 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 1 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 1 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 1 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DA 2 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 2 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 2 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 3 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 3 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 4 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 4 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 4 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 5 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 5 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 6 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 6 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 6 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 7 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 7 B DA 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 8 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 8 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 9 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 9 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 9 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1DK9 _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 1DK9 _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 DA 2 2 2 DA ADE A . n A 1 3 DT 3 3 3 DT THY A . n A 1 4 DG 4 4 4 DG GUA A . n A 1 5 DA 5 5 5 DA ADE A . n A 1 6 DG 6 6 6 DG GUA A . n A 1 7 DT 7 7 7 DT THY A . n A 1 8 DA 8 8 8 DA ADE A . n A 1 9 DC 9 9 9 DC CYT A . n B 2 1 DG 1 10 10 DG GUA B . n B 2 2 DT 2 11 11 DT THY B . n B 2 3 DA 3 12 12 DA ADE B . n B 2 4 DC 4 13 13 DC CYT B . n B 2 5 DT 5 14 14 DT THY B . n B 2 6 DC 6 15 15 DC CYT B . n B 2 7 DA 7 16 16 DA ADE B . n B 2 8 DT 8 17 17 DT THY B . n B 2 9 DG 9 18 18 DG GUA 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 1999-12-16 2 'Structure model' 1 1 2008-04-27 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' # 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_struct_assembly 3 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' # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 H21 A DG 6 ? ? O2 B DC 13 ? ? 1.40 2 1 H21 A DG 4 ? ? O2 B DC 15 ? ? 1.47 3 1 O2 A DC 1 ? ? H21 B DG 18 ? ? 1.48 4 1 O2 A DC 9 ? ? H21 B DG 10 ? ? 1.50 5 1 O6 A DG 4 ? ? H41 B DC 15 ? ? 1.50 6 1 H41 A DC 9 ? ? O6 B DG 10 ? ? 1.54 7 1 H1 A DG 6 ? ? N3 B DC 13 ? ? 1.54 8 1 H1 A DG 4 ? ? N3 B DC 15 ? ? 1.55 9 1 N1 A DA 8 ? ? H3 B DT 11 ? ? 1.56 10 1 N1 A DA 5 ? ? H3 B DT 14 ? ? 1.56 11 1 N1 A DA 2 ? ? H3 B DT 17 ? ? 1.58 12 1 O6 A DG 6 ? ? H41 B DC 13 ? ? 1.58 13 1 N3 A DC 1 ? ? H1 B DG 18 ? ? 1.58 14 1 O4 A DT 7 ? ? H61 B DA 12 ? ? 1.59 15 1 H3 A DT 7 ? ? N1 B DA 12 ? ? 1.59 # 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 C5 A DT 7 ? ? C7 A DT 7 ? ? 1.542 1.496 0.046 0.006 N 2 1 C5 B DT 17 ? ? C7 B DT 17 ? ? 1.534 1.496 0.038 0.006 N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.92 108.30 3.62 0.30 N 2 1 N7 A DG 4 ? ? C8 A DG 4 ? ? N9 A DG 4 ? ? 116.41 113.10 3.31 0.50 N 3 1 "O4'" A DA 5 ? ? "C1'" A DA 5 ? ? N9 A DA 5 ? ? 112.91 108.30 4.61 0.30 N 4 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 112.10 108.30 3.80 0.30 N 5 1 N7 A DG 6 ? ? C8 A DG 6 ? ? N9 A DG 6 ? ? 116.73 113.10 3.63 0.50 N 6 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 103.23 108.00 -4.77 0.70 N 7 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? "C2'" A DC 9 ? ? 100.44 105.90 -5.46 0.80 N 8 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 114.23 108.30 5.93 0.30 N 9 1 N7 B DG 10 ? ? C8 B DG 10 ? ? N9 B DG 10 ? ? 116.59 113.10 3.49 0.50 N 10 1 "O4'" B DT 11 ? ? "C1'" B DT 11 ? ? N1 B DT 11 ? ? 116.02 108.30 7.72 0.30 N 11 1 C6 B DT 11 ? ? C5 B DT 11 ? ? C7 B DT 11 ? ? 116.69 122.90 -6.21 0.60 N 12 1 "O4'" B DA 12 ? ? "C1'" B DA 12 ? ? N9 B DA 12 ? ? 110.20 108.30 1.90 0.30 N 13 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 111.82 108.30 3.52 0.30 N 14 1 N7 B DA 16 ? ? C8 B DA 16 ? ? N9 B DA 16 ? ? 117.13 113.80 3.33 0.50 N 15 1 C6 B DT 17 ? ? C5 B DT 17 ? ? C7 B DT 17 ? ? 119.27 122.90 -3.63 0.60 N 16 1 "C1'" B DG 18 ? ? "O4'" B DG 18 ? ? "C4'" B DG 18 ? ? 104.07 110.10 -6.03 1.00 N 17 1 "O4'" B DG 18 ? ? "C1'" B DG 18 ? ? N9 B DG 18 ? ? 110.85 108.30 2.55 0.30 N 18 1 N7 B DG 18 ? ? C8 B DG 18 ? ? N9 B DG 18 ? ? 116.18 113.10 3.08 0.50 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1DK9 'double helix' 1DK9 '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 9 1_555 0.299 -0.468 0.156 11.032 -20.539 0.988 1 A_DC1:DG18_B A 1 ? B 18 ? 19 1 1 A DA 2 1_555 B DT 8 1_555 0.108 -0.357 0.360 3.758 -9.696 4.559 2 A_DA2:DT17_B A 2 ? B 17 ? 20 1 1 A DT 3 1_555 B DA 7 1_555 0.124 -0.326 0.573 1.353 -12.621 10.682 3 A_DT3:DA16_B A 3 ? B 16 ? 20 1 1 A DG 4 1_555 B DC 6 1_555 -0.157 -0.485 0.084 3.994 -1.764 -0.372 4 A_DG4:DC15_B A 4 ? B 15 ? 19 1 1 A DA 5 1_555 B DT 5 1_555 0.296 -0.370 -0.111 -1.271 -7.882 3.075 5 A_DA5:DT14_B A 5 ? B 14 ? 20 1 1 A DG 6 1_555 B DC 4 1_555 -0.273 -0.508 0.136 -5.926 -10.084 2.040 6 A_DG6:DC13_B A 6 ? B 13 ? 19 1 1 A DT 7 1_555 B DA 3 1_555 -0.083 -0.359 0.069 -15.253 -0.937 -1.035 7 A_DT7:DA12_B A 7 ? B 12 ? 20 1 1 A DA 8 1_555 B DT 2 1_555 0.043 -0.377 -0.264 -15.567 -3.001 1.908 8 A_DA8:DT11_B A 8 ? B 11 ? 20 1 1 A DC 9 1_555 B DG 1 1_555 0.324 -0.466 0.302 -11.700 2.336 -0.778 9 A_DC9:DG10_B A 9 ? B 10 ? 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 9 1_555 A DA 2 1_555 B DT 8 1_555 -0.296 -1.368 2.928 -3.550 11.459 30.144 -4.125 0.012 2.288 21.018 6.512 32.392 1 AA_DC1DA2:DT17DG18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A DA 2 1_555 B DT 8 1_555 A DT 3 1_555 B DA 7 1_555 0.290 -0.913 3.109 -0.842 -5.535 37.038 -0.717 -0.559 3.201 -8.652 1.316 37.445 2 AA_DA2DT3:DA16DT17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A DT 3 1_555 B DA 7 1_555 A DG 4 1_555 B DC 6 1_555 -0.248 -0.825 2.799 2.620 1.327 37.794 -1.414 0.667 2.747 2.044 -4.038 37.904 3 AA_DT3DG4:DC15DA16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A DG 4 1_555 B DC 6 1_555 A DA 5 1_555 B DT 5 1_555 0.103 -0.842 3.104 2.900 3.535 40.506 -1.576 0.153 3.023 5.086 -4.172 40.752 4 AA_DG4DA5:DT14DC15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A DA 5 1_555 B DT 5 1_555 A DG 6 1_555 B DC 4 1_555 -0.182 -1.149 3.075 -2.708 3.553 34.696 -2.408 -0.075 2.952 5.928 4.518 34.973 5 AA_DA5DG6:DC13DT14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A DG 6 1_555 B DC 4 1_555 A DT 7 1_555 B DA 3 1_555 -0.119 -1.051 3.308 3.786 -5.527 42.438 -0.871 0.550 3.390 -7.579 -5.191 42.940 6 AA_DG6DT7:DA12DC13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A DT 7 1_555 B DA 3 1_555 A DA 8 1_555 B DT 2 1_555 0.385 -0.621 2.988 4.238 7.570 39.265 -1.682 -0.125 2.850 11.101 -6.214 40.176 7 AA_DT7DA8:DT11DA12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DA 8 1_555 B DT 2 1_555 A DC 9 1_555 B DG 1 1_555 0.252 -0.624 3.047 -4.660 -2.074 29.665 -0.807 -1.374 3.009 -4.014 9.018 30.090 8 AA_DA8DC9:DG10DT11_BB A 8 ? B 11 ? A 9 ? B 10 ? #