data_1K9H # _entry.id 1K9H # _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 1K9H pdb_00001k9h 10.2210/pdb1k9h/pdb RCSB RCSB014727 ? ? WWPDB D_1000014727 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1k9l _pdbx_database_related.details '1k9l is the Solution structure of the DNA oligomer TATGAGCGCTCATA.' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1K9H _pdbx_database_status.recvd_initial_deposition_date 2001-10-29 _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 'Kaluarachchi, K.' 1 'Gorenstein, D.G.' 2 'Luxon, B.A.' 3 # _citation.id primary _citation.title 'How Do Proteins Recognize DNA? Solution Structure and Local Conformational Dynamics of Lac Operators by 2D NMR' _citation.journal_abbrev J.Biomol.Struct.Dyn. _citation.journal_volume 'Conversation 11' _citation.page_first 123 _citation.page_last 133 _citation.year 2000 _citation.journal_id_ASTM JBSDD6 _citation.country US _citation.journal_id_ISSN 0739-1102 _citation.journal_id_CSD 0646 _citation.book_publisher ? _citation.pdbx_database_id_PubMed -1 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Kaluarachchi, K.' 1 ? primary 'Gorenstein, D.G.' 2 ? primary 'Luxon, B.A.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description "5'-D(*TP*GP*TP*GP*AP*GP*CP*GP*CP*TP*CP*AP*CP*A)-3'" _entity.formula_weight 4280.792 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ;This sequence has been derived from the natural Lac Operator sequence by symmetrizing the minimum required length for lac repressor binding. ; # _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 '(DT)(DG)(DT)(DG)(DA)(DG)(DC)(DG)(DC)(DT)(DC)(DA)(DC)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TGTGAGCGCTCACA _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 DT n 1 2 DG n 1 3 DT n 1 4 DG n 1 5 DA n 1 6 DG n 1 7 DC n 1 8 DG n 1 9 DC n 1 10 DT n 1 11 DC n 1 12 DA n 1 13 DC n 1 14 DA n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1K9H _struct_ref.pdbx_db_accession 1K9H _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1K9H A 1 ? 14 ? 1K9H 1 ? 14 ? 1 14 2 1 1K9H B 1 ? 14 ? 1K9H 15 ? 28 ? 15 28 # 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.solution_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type 1 1 1 '2D NOESY' 2 1 1 '2D TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pH 7.4 _pdbx_nmr_exptl_sample_conditions.ionic_strength '150 mM KCl' _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 '3.6 mM oligonucleotide, 55 mM potassium phosphate, 150 mM KCl, 0.1mM NaN3' _pdbx_nmr_sample_details.solvent_system '99.96% D2O' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.field_strength 1 ? Varian VXRS 500 2 ? Varian VXRS 600 # _pdbx_nmr_refine.entry_id 1K9H _pdbx_nmr_refine.method ;molecular dynamics, matrix relaxation, simulated annealing ; _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1K9H _pdbx_nmr_details.text 'This structure was determined using standard homonuclear techniques.' # _pdbx_nmr_ensemble.entry_id 1K9H _pdbx_nmr_ensemble.conformers_calculated_total_number 2 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'back calculated data agree with experimental NOESY spectrum,structures with the lowest energy' _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 ? # _pdbx_nmr_representative.entry_id 1K9H _pdbx_nmr_representative.conformer_id ? _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal Amber 'versions 3-5' refinement 'Kollman. P.' 1 MORASS 1.0 refinement 'Meadows. R.P.' 2 # _exptl.entry_id 1K9H _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1K9H _struct.title 'NMR structure of DNA TGTGAGCGCTCACA' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1K9H _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'Lac operator, Double helix, 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 ? # _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 DT 1 N3 ? ? ? 1_555 B DA 14 N1 ? ? A DT 1 B DA 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DT 1 O4 ? ? ? 1_555 B DA 14 N6 ? ? A DT 1 B DA 28 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 13 N3 ? ? A DG 2 B DC 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 13 O2 ? ? A DG 2 B DC 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 13 N4 ? ? A DG 2 B DC 27 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 12 N1 ? ? A DT 3 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 12 N6 ? ? A DT 3 B DA 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 4 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 4 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 4 B DC 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 10 N3 ? ? A DA 5 B DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 10 O4 ? ? A DA 5 B DT 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 6 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 6 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 6 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B DG 8 N1 ? ? A DC 7 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 8 O6 ? ? A DC 7 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B DG 8 N2 ? ? A DC 7 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 7 N3 ? ? A DG 8 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 7 O2 ? ? A DG 8 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 8 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 9 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 9 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 9 B DG 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 10 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 10 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 11 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DA 12 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 12 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DA 12 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 12 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DC 13 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 13 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog33 hydrog ? ? A DC 13 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 13 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog34 hydrog ? ? A DC 13 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 13 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog35 hydrog ? ? A DA 14 N1 ? ? ? 1_555 B DT 1 N3 ? ? A DA 14 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog36 hydrog ? ? A DA 14 N6 ? ? ? 1_555 B DT 1 O4 ? ? A DA 14 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1K9H _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 1K9H _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 DT 1 1 1 DT THY A . n A 1 2 DG 2 2 2 DG GUA 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 DC 7 7 7 DC CYT A . n A 1 8 DG 8 8 8 DG GUA A . n A 1 9 DC 9 9 9 DC CYT A . n A 1 10 DT 10 10 10 DT THY A . n A 1 11 DC 11 11 11 DC CYT A . n A 1 12 DA 12 12 12 DA ADE A . n A 1 13 DC 13 13 13 DC CYT A . n A 1 14 DA 14 14 14 DA ADE A . n B 1 1 DT 1 15 15 DT THY B . n B 1 2 DG 2 16 16 DG GUA B . n B 1 3 DT 3 17 17 DT THY B . n B 1 4 DG 4 18 18 DG GUA B . n B 1 5 DA 5 19 19 DA ADE B . n B 1 6 DG 6 20 20 DG GUA B . n B 1 7 DC 7 21 21 DC CYT B . n B 1 8 DG 8 22 22 DG GUA B . n B 1 9 DC 9 23 23 DC CYT B . n B 1 10 DT 10 24 24 DT THY B . n B 1 11 DC 11 25 25 DC CYT B . n B 1 12 DA 12 26 26 DA ADE B . n B 1 13 DC 13 27 27 DC CYT B . n B 1 14 DA 14 28 28 DA ADE 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 2001-11-07 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-23 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_nmr_software 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_nmr_software.name' # 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 "O5'" A DT 1 ? ? "C5'" A DT 1 ? ? 1.047 1.418 -0.371 0.025 N 2 1 "O4'" A DT 1 ? ? "C4'" A DT 1 ? ? 1.375 1.446 -0.071 0.010 N 3 1 "O3'" A DT 1 ? ? "C3'" A DT 1 ? ? 1.378 1.419 -0.041 0.006 N 4 1 "O4'" A DT 3 ? ? "C4'" A DT 3 ? ? 1.383 1.446 -0.063 0.010 N 5 1 P A DC 9 ? ? OP1 A DC 9 ? ? 1.353 1.485 -0.132 0.017 N 6 1 P A DC 9 ? ? "O5'" A DC 9 ? ? 1.468 1.593 -0.125 0.010 N 7 1 "O4'" A DC 9 ? ? "C4'" A DC 9 ? ? 1.384 1.446 -0.062 0.010 N 8 1 "O4'" B DT 15 ? ? "C4'" B DT 15 ? ? 1.378 1.446 -0.068 0.010 N 9 1 "O4'" B DT 24 ? ? "C4'" B DT 24 ? ? 1.386 1.446 -0.060 0.010 N 10 1 "O3'" B DA 28 ? ? "C3'" B DA 28 ? ? 1.369 1.419 -0.050 0.006 N 11 1 C4 B DA 28 ? ? C5 B DA 28 ? ? 1.337 1.383 -0.046 0.007 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 DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 112.16 108.30 3.86 0.30 N 2 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 116.51 108.30 8.21 0.30 N 3 1 N7 A DG 4 ? ? C8 A DG 4 ? ? N9 A DG 4 ? ? 116.28 113.10 3.18 0.50 N 4 1 C8 A DG 4 ? ? N9 A DG 4 ? ? C4 A DG 4 ? ? 103.16 106.40 -3.24 0.40 N 5 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.15 108.30 1.85 0.30 N 6 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.96 108.30 3.66 0.30 N 7 1 P A DC 9 ? ? "O5'" A DC 9 ? ? "C5'" A DC 9 ? ? 135.89 120.90 14.99 1.60 N 8 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 110.35 108.30 2.05 0.30 N 9 1 "C4'" A DT 10 ? ? "C3'" A DT 10 ? ? "C2'" A DT 10 ? ? 97.95 102.20 -4.25 0.70 N 10 1 "C3'" A DT 10 ? ? "C2'" A DT 10 ? ? "C1'" A DT 10 ? ? 110.43 102.50 7.93 1.20 N 11 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 111.48 108.30 3.18 0.30 N 12 1 "O4'" A DA 12 ? ? "C4'" A DA 12 ? ? "C3'" A DA 12 ? ? 110.48 106.00 4.48 0.60 N 13 1 "C4'" A DA 12 ? ? "C3'" A DA 12 ? ? "C2'" A DA 12 ? ? 92.30 102.20 -9.90 0.70 N 14 1 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? "C2'" A DA 12 ? ? 100.97 105.90 -4.93 0.80 N 15 1 "O4'" A DA 12 ? ? "C1'" A DA 12 ? ? N9 A DA 12 ? ? 112.60 108.30 4.30 0.30 N 16 1 "O4'" A DC 13 ? ? "C1'" A DC 13 ? ? N1 A DC 13 ? ? 111.94 108.30 3.64 0.30 N 17 1 "O4'" A DA 14 ? ? "C1'" A DA 14 ? ? N9 A DA 14 ? ? 111.19 108.30 2.89 0.30 N 18 1 "O4'" B DT 15 ? ? "C1'" B DT 15 ? ? N1 B DT 15 ? ? 110.71 108.30 2.41 0.30 N 19 1 "O4'" B DG 18 ? ? "C1'" B DG 18 ? ? N9 B DG 18 ? ? 115.86 108.30 7.56 0.30 N 20 1 C8 B DG 18 ? ? N9 B DG 18 ? ? C4 B DG 18 ? ? 103.91 106.40 -2.49 0.40 N 21 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 111.54 108.30 3.24 0.30 N 22 1 "O4'" B DT 24 ? ? "C4'" B DT 24 ? ? "C3'" B DT 24 ? ? 110.24 106.00 4.24 0.60 N 23 1 "C4'" B DT 24 ? ? "C3'" B DT 24 ? ? "C2'" B DT 24 ? ? 97.27 102.20 -4.93 0.70 N 24 1 "C3'" B DT 24 ? ? "C2'" B DT 24 ? ? "C1'" B DT 24 ? ? 110.49 102.50 7.99 1.20 N 25 1 "O4'" B DC 25 ? ? "C1'" B DC 25 ? ? N1 B DC 25 ? ? 113.01 108.30 4.71 0.30 N 26 1 "O4'" B DC 27 ? ? "C1'" B DC 27 ? ? N1 B DC 27 ? ? 111.16 108.30 2.86 0.30 N 27 1 "O4'" B DA 28 ? ? "C1'" B DA 28 ? ? N9 B DA 28 ? ? 110.68 108.30 2.38 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 4 ? ? 0.079 'SIDE CHAIN' 2 1 DA A 5 ? ? 0.076 'SIDE CHAIN' 3 1 DC A 7 ? ? 0.074 'SIDE CHAIN' 4 1 DA A 12 ? ? 0.094 'SIDE CHAIN' 5 1 DT B 15 ? ? 0.088 'SIDE CHAIN' 6 1 DG B 16 ? ? 0.067 'SIDE CHAIN' 7 1 DG B 18 ? ? 0.097 'SIDE CHAIN' 8 1 DA B 19 ? ? 0.056 'SIDE CHAIN' 9 1 DC B 25 ? ? 0.093 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1K9H 'double helix' 1K9H '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 DT 1 1_555 B DA 14 1_555 0.419 -0.183 -0.275 23.054 -41.343 5.687 1 A_DT1:DA28_B A 1 ? B 28 ? 20 1 1 A DG 2 1_555 B DC 13 1_555 -0.382 -0.265 0.143 -5.776 -8.346 -0.940 2 A_DG2:DC27_B A 2 ? B 27 ? 19 1 1 A DT 3 1_555 B DA 12 1_555 0.110 -0.202 0.185 -2.009 -12.567 3.780 3 A_DT3:DA26_B A 3 ? B 26 ? 20 1 1 A DG 4 1_555 B DC 11 1_555 -0.391 -0.336 -0.715 -21.363 -28.448 0.029 4 A_DG4:DC25_B A 4 ? B 25 ? 19 1 1 A DA 5 1_555 B DT 10 1_555 -0.074 -0.127 -0.416 -27.297 -13.066 3.054 5 A_DA5:DT24_B A 5 ? B 24 ? 20 1 1 A DG 6 1_555 B DC 9 1_555 -0.264 -0.214 0.095 -3.060 -7.235 -0.151 6 A_DG6:DC23_B A 6 ? B 23 ? 19 1 1 A DC 7 1_555 B DG 8 1_555 0.195 -0.255 0.282 -11.475 0.479 -3.467 7 A_DC7:DG22_B A 7 ? B 22 ? 19 1 1 A DG 8 1_555 B DC 7 1_555 -0.155 -0.232 0.426 13.643 1.109 -2.777 8 A_DG8:DC21_B A 8 ? B 21 ? 19 1 1 A DC 9 1_555 B DG 6 1_555 0.278 -0.218 0.039 4.128 -6.864 -0.502 9 A_DC9:DG20_B A 9 ? B 20 ? 19 1 1 A DT 10 1_555 B DA 5 1_555 0.039 -0.161 0.239 7.988 -1.703 5.300 10 A_DT10:DA19_B A 10 ? B 19 ? 20 1 1 A DC 11 1_555 B DG 4 1_555 0.326 -0.287 0.106 1.895 -14.175 -3.053 11 A_DC11:DG18_B A 11 ? B 18 ? 19 1 1 A DA 12 1_555 B DT 3 1_555 -0.266 -0.277 0.226 2.525 -13.667 -2.326 12 A_DA12:DT17_B A 12 ? B 17 ? 20 1 1 A DC 13 1_555 B DG 2 1_555 0.528 -0.241 0.404 1.562 -6.546 1.339 13 A_DC13:DG16_B A 13 ? B 16 ? 19 1 1 A DA 14 1_555 B DT 1 1_555 -0.011 -0.216 0.050 0.170 -31.247 -3.574 14 A_DA14:DT15_B A 14 ? B 15 ? 20 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 DT 1 1_555 B DA 14 1_555 A DG 2 1_555 B DC 13 1_555 -0.828 -0.548 3.619 -8.301 25.932 38.638 -3.044 0.285 2.855 34.482 11.039 46.966 1 AA_DT1DG2:DC27DA28_BB A 1 ? B 28 ? A 2 ? B 27 ? 1 A DG 2 1_555 B DC 13 1_555 A DT 3 1_555 B DA 12 1_555 0.013 -0.381 3.127 0.075 4.692 35.096 -1.281 -0.011 3.053 7.738 -0.124 35.399 2 AA_DG2DT3:DA26DC27_BB A 2 ? B 27 ? A 3 ? B 26 ? 1 A DT 3 1_555 B DA 12 1_555 A DG 4 1_555 B DC 11 1_555 0.193 -0.501 3.575 8.931 17.661 33.338 -3.094 0.889 2.922 27.937 -14.128 38.626 3 AA_DT3DG4:DC25DA26_BB A 3 ? B 26 ? A 4 ? B 25 ? 1 A DG 4 1_555 B DC 11 1_555 A DA 5 1_555 B DT 10 1_555 0.464 -0.003 3.296 -1.030 4.830 33.004 -0.811 -0.980 3.247 8.443 1.801 33.361 4 AA_DG4DA5:DT24DC25_BB A 4 ? B 25 ? A 5 ? B 24 ? 1 A DA 5 1_555 B DT 10 1_555 A DG 6 1_555 B DC 9 1_555 -0.451 -0.262 2.808 -9.311 15.802 27.129 -2.840 -0.595 2.345 29.758 17.534 32.651 5 AA_DA5DG6:DC23DT24_BB A 5 ? B 24 ? A 6 ? B 23 ? 1 A DG 6 1_555 B DC 9 1_555 A DC 7 1_555 B DG 8 1_555 -0.481 -0.633 3.432 -1.743 4.638 40.741 -1.430 0.488 3.360 6.633 2.493 41.028 6 AA_DG6DC7:DG22DC23_BB A 6 ? B 23 ? A 7 ? B 22 ? 1 A DC 7 1_555 B DG 8 1_555 A DG 8 1_555 B DC 7 1_555 0.002 -0.427 2.634 -2.161 0.134 26.826 -0.944 -0.450 2.623 0.289 4.649 26.912 7 AA_DC7DG8:DC21DG22_BB A 7 ? B 22 ? A 8 ? B 21 ? 1 A DG 8 1_555 B DC 7 1_555 A DC 9 1_555 B DG 6 1_555 0.525 -0.433 3.469 3.846 2.505 39.497 -0.946 -0.297 3.470 3.692 -5.667 39.753 8 AA_DG8DC9:DG20DC21_BB A 8 ? B 21 ? A 9 ? B 20 ? 1 A DC 9 1_555 B DG 6 1_555 A DT 10 1_555 B DA 5 1_555 1.206 -0.133 3.481 6.517 28.880 26.248 -3.984 -0.936 2.447 48.121 -10.858 39.370 9 AA_DC9DT10:DA19DG20_BB A 9 ? B 20 ? A 10 ? B 19 ? 1 A DT 10 1_555 B DA 5 1_555 A DC 11 1_555 B DG 4 1_555 -0.270 -0.140 3.373 1.731 11.026 30.942 -2.183 0.781 3.123 19.873 -3.120 32.847 10 AA_DT10DC11:DG18DA19_BB A 10 ? B 19 ? A 11 ? B 18 ? 1 A DC 11 1_555 B DG 4 1_555 A DA 12 1_555 B DT 3 1_555 -0.502 -0.357 3.144 -1.687 5.252 32.343 -1.495 0.612 3.072 9.343 3.001 32.798 11 AA_DC11DA12:DT17DG18_BB A 11 ? B 18 ? A 12 ? B 17 ? 1 A DA 12 1_555 B DT 3 1_555 A DC 13 1_555 B DG 2 1_555 0.225 0.038 3.347 -1.566 0.685 37.476 -0.033 -0.559 3.335 1.065 2.435 37.514 12 AA_DA12DC13:DG16DT17_BB A 12 ? B 17 ? A 13 ? B 16 ? 1 A DC 13 1_555 B DG 2 1_555 A DA 14 1_555 B DT 1 1_555 0.406 -0.300 3.157 7.939 11.693 30.083 -2.427 0.581 2.862 21.124 -14.343 33.169 13 AA_DC13DA14:DT15DG16_BB A 13 ? B 16 ? A 14 ? B 15 ? #