data_1SKP # _entry.id 1SKP # _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 1SKP pdb_00001skp 10.2210/pdb1skp/pdb WWPDB D_1000176401 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1SKP _pdbx_database_status.recvd_initial_deposition_date 1998-05-20 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _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 'Tonelli, M.' 1 'Ragg, E.' 2 'Bianucci, A.M.' 3 'Lesiak, K.' 4 'James, T.L.' 5 # _citation.id primary _citation.title ;Nuclear magnetic resonance structure of d(GCATATGATAG). d(CTATCATATGC): a consensus sequence for promoters recognized by sigma K RNA polymerase. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 37 _citation.page_first 11745 _citation.page_last 11761 _citation.year 1998 _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 9718297 _citation.pdbx_database_id_DOI 10.1021/bi980481n # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Tonelli, M.' 1 ? primary 'Ragg, E.' 2 ? primary 'Bianucci, A.M.' 3 ? primary 'Lesiak, K.' 4 ? primary 'James, T.L.' 5 ? # _cell.entry_id 1SKP _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 1SKP _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 'SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE' 3397.247 1 ? ? ? ? 2 polymer syn 'SIGMA-K RNA POLYMERASE CONSENSUS SEQUENCE' 3308.185 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)(DA)(DT)(DA)(DT)(DG)(DA)(DT)(DA)(DG)' GCATATGATAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DA)(DT)(DC)(DA)(DT)(DA)(DT)(DG)(DC)' CTATCATATGC 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 DA n 1 4 DT n 1 5 DA n 1 6 DT n 1 7 DG n 1 8 DA n 1 9 DT n 1 10 DA n 1 11 DG n 2 1 DC n 2 2 DT n 2 3 DA n 2 4 DT n 2 5 DC n 2 6 DA n 2 7 DT n 2 8 DA n 2 9 DT n 2 10 DG n 2 11 DC n # 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 1SKP 1SKP ? ? ? 2 2 PDB 1SKP 1SKP ? ? ? # 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 1SKP A 1 ? 11 ? 1SKP 1 ? 11 ? 1 11 2 2 1SKP B 1 ? 11 ? 1SKP 12 ? 22 ? 12 22 # 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.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 COSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength '0.5 M' _pdbx_nmr_exptl_sample_conditions.pressure_units ATMOSPHERE _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents 'H2O AND D2O' # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AMX600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 1SKP _pdbx_nmr_refine.method 'MOLECULAR DYNAMIC (RMD) AND MONTE CARLO (RMC) CALCULATIONS' _pdbx_nmr_refine.details ;REFINEMENT DETAILS CAN BE FOUND IN THE BIOCHEMISTRY CITATION ABOVE. MODEL 1 : REFINED BY RMD FROM A-DNA MODEL 2 : REFINED BY RMD FROM B-DNA MODEL 3 : REFINED BY RMC FROM A-DNA MODEL 4 : REFINED BY RMC FROM B-DNA ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1SKP _pdbx_nmr_details.text 'STRUCTURE DETERMINED WITH HOMONUCLEAR NMR METHODS.' # _pdbx_nmr_ensemble.entry_id 1SKP _pdbx_nmr_ensemble.conformers_calculated_total_number 20 _pdbx_nmr_ensemble.conformers_submitted_total_number 4 _pdbx_nmr_ensemble.conformer_selection_criteria 'CONVERGENCE, R FACTORS, ENERGIES' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement MARDIGRAS ? PEARLMAN 1 'structure solution' MARDIGRAS ? ? 2 'structure solution' Amber ? ? 3 'structure solution' DNAminiCarlo ? ? 4 # _exptl.entry_id 1SKP _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1SKP _struct.title ;NMR STRUCTURE OF D(GCATATGATAG)(DOT)D(CTATCATATGC): A CONSENSUS SEQUENCE FOR PROMOTERS RECOGNIZED BY SIGMA-K RNA POLYMERASE, 4 STRUCTURES ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1SKP _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'PROMOTER SEQUENCE, 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 ? # _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 DG 1 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 1 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 1 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 1 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 2 B DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 2 B DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 2 B DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 3 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 3 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 4 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 4 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 5 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 5 B DT 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 6 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 6 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 7 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 7 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 7 B DC 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 8 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 8 B DT 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 9 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 9 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 10 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 10 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1SKP _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 1SKP _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 G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DT 9 9 9 DT T A . n A 1 10 DA 10 10 10 DA A A . n A 1 11 DG 11 11 11 DG G A . n B 2 1 DC 1 12 12 DC C B . n B 2 2 DT 2 13 13 DT T B . n B 2 3 DA 3 14 14 DA A B . n B 2 4 DT 4 15 15 DT T B . n B 2 5 DC 5 16 16 DC C B . n B 2 6 DA 6 17 17 DA A B . n B 2 7 DT 7 18 18 DT T B . n B 2 8 DA 8 19 19 DA A B . n B 2 9 DT 9 20 20 DT T B . n B 2 10 DG 10 21 21 DG G B . n B 2 11 DC 11 22 22 DC C 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 1999-01-13 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-02 # _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' 6 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_nmr_software 4 4 'Structure model' pdbx_struct_assembly 5 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' 4 4 'Structure model' '_pdbx_nmr_software.name' # _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 DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 113.46 108.30 5.16 0.30 N 2 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? "C2'" A DT 4 ? ? 99.91 105.90 -5.99 0.80 N 3 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 114.36 108.30 6.06 0.30 N 4 1 C4 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 123.86 119.00 4.86 0.60 N 5 1 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 115.22 122.90 -7.68 0.60 N 6 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 111.85 108.30 3.55 0.30 N 7 1 "O4'" A DA 8 ? ? "C4'" A DA 8 ? ? "C3'" A DA 8 ? ? 110.01 106.00 4.01 0.60 N 8 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.82 108.30 2.52 0.30 N 9 1 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 117.71 122.90 -5.19 0.60 N 10 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 111.89 108.30 3.59 0.30 N 11 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 110.85 108.30 2.55 0.30 N 12 1 C6 B DT 13 ? ? C5 B DT 13 ? ? C7 B DT 13 ? ? 117.31 122.90 -5.59 0.60 N 13 1 C6 B DT 15 ? ? C5 B DT 15 ? ? C7 B DT 15 ? ? 119.24 122.90 -3.66 0.60 N 14 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 113.96 108.30 5.66 0.30 N 15 1 N1 B DA 17 ? ? C6 B DA 17 ? ? N6 B DA 17 ? ? 122.28 118.60 3.68 0.60 N 16 1 C5 B DA 17 ? ? C6 B DA 17 ? ? N6 B DA 17 ? ? 118.30 123.70 -5.40 0.80 N 17 1 "O4'" B DT 18 ? ? "C1'" B DT 18 ? ? N1 B DT 18 ? ? 111.02 108.30 2.72 0.30 N 18 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 110.71 108.30 2.41 0.30 N 19 1 C6 B DT 20 ? ? C5 B DT 20 ? ? C7 B DT 20 ? ? 117.55 122.90 -5.35 0.60 N 20 1 "O4'" B DG 21 ? ? "C1'" B DG 21 ? ? N9 B DG 21 ? ? 111.16 108.30 2.86 0.30 N 21 2 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 113.23 108.30 4.93 0.30 N 22 2 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 110.80 108.30 2.50 0.30 N 23 2 C4 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 123.00 119.00 4.00 0.60 N 24 2 C6 A DT 4 ? ? C5 A DT 4 ? ? C7 A DT 4 ? ? 115.25 122.90 -7.65 0.60 N 25 2 "O4'" A DA 5 ? ? "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? 110.19 106.00 4.19 0.60 N 26 2 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 112.73 108.30 4.43 0.30 N 27 2 "O4'" A DA 8 ? ? "C4'" A DA 8 ? ? "C3'" A DA 8 ? ? 110.11 106.00 4.11 0.60 N 28 2 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.40 108.30 2.10 0.30 N 29 2 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 117.66 122.90 -5.24 0.60 N 30 2 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 114.42 108.30 6.12 0.30 N 31 2 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 113.26 108.30 4.96 0.30 N 32 2 C6 B DT 13 ? ? C5 B DT 13 ? ? C7 B DT 13 ? ? 117.81 122.90 -5.09 0.60 N 33 2 C6 B DT 15 ? ? C5 B DT 15 ? ? C7 B DT 15 ? ? 118.98 122.90 -3.92 0.60 N 34 2 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 111.55 108.30 3.25 0.30 N 35 2 C5 B DA 17 ? ? C6 B DA 17 ? ? N6 B DA 17 ? ? 118.63 123.70 -5.07 0.80 N 36 2 C6 B DT 18 ? ? C5 B DT 18 ? ? C7 B DT 18 ? ? 119.09 122.90 -3.81 0.60 N 37 2 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 110.32 108.30 2.02 0.30 N 38 2 C6 B DT 20 ? ? C5 B DT 20 ? ? C7 B DT 20 ? ? 117.64 122.90 -5.26 0.60 N 39 2 "C3'" B DG 21 ? ? "O3'" B DG 21 ? ? P B DC 22 ? ? 127.25 119.70 7.55 1.20 Y 40 2 "O4'" B DC 22 ? ? "C1'" B DC 22 ? ? N1 B DC 22 ? ? 110.41 108.30 2.11 0.30 N 41 3 "C3'" A DG 1 ? ? "O3'" A DG 1 ? ? P A DC 2 ? ? 131.55 119.70 11.85 1.20 Y 42 4 "O4'" A DG 1 ? ? "C4'" A DG 1 ? ? "C3'" A DG 1 ? ? 101.18 104.50 -3.32 0.40 N 43 4 "C3'" A DG 1 ? ? "O3'" A DG 1 ? ? P A DC 2 ? ? 128.68 119.70 8.98 1.20 Y # 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 DT A 4 ? ? 0.121 'SIDE CHAIN' 2 1 DA A 10 ? ? 0.072 'SIDE CHAIN' 3 1 DG A 11 ? ? 0.059 'SIDE CHAIN' 4 1 DA B 17 ? ? 0.092 'SIDE CHAIN' 5 1 DG B 21 ? ? 0.051 'SIDE CHAIN' 6 2 DT A 4 ? ? 0.098 'SIDE CHAIN' 7 2 DG B 21 ? ? 0.052 'SIDE CHAIN' 8 2 DC B 22 ? ? 0.086 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1SKP 'double helix' 1SKP '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 DG 1 1_555 B DC 11 1_555 -0.495 -0.178 0.363 20.706 4.289 -0.940 1 A_DG1:DC22_B A 1 ? B 22 ? 19 1 1 A DC 2 1_555 B DG 10 1_555 0.522 -0.334 0.040 14.116 -17.382 -4.235 2 A_DC2:DG21_B A 2 ? B 21 ? 19 1 1 A DA 3 1_555 B DT 9 1_555 0.376 -0.123 0.279 -0.876 -14.773 -6.571 3 A_DA3:DT20_B A 3 ? B 20 ? 20 1 1 A DT 4 1_555 B DA 8 1_555 0.282 -0.219 0.658 -12.723 -9.728 0.107 4 A_DT4:DA19_B A 4 ? B 19 ? 20 1 1 A DA 5 1_555 B DT 7 1_555 -0.223 -0.154 -0.041 0.430 -8.353 -4.402 5 A_DA5:DT18_B A 5 ? B 18 ? 20 1 1 A DT 6 1_555 B DA 6 1_555 -0.636 0.036 0.078 9.476 -7.834 -12.494 6 A_DT6:DA17_B A 6 ? B 17 ? 20 1 1 A DG 7 1_555 B DC 5 1_555 -0.546 -0.286 0.340 11.103 -7.608 -2.025 7 A_DG7:DC16_B A 7 ? B 16 ? 19 1 1 A DA 8 1_555 B DT 4 1_555 0.077 -0.193 -0.191 -4.393 -17.826 -3.007 8 A_DA8:DT15_B A 8 ? B 15 ? 20 1 1 A DT 9 1_555 B DA 3 1_555 0.014 -0.157 0.117 -2.713 -15.076 1.261 9 A_DT9:DA14_B A 9 ? B 14 ? 20 1 1 A DA 10 1_555 B DT 2 1_555 0.507 -0.059 -0.365 -16.883 -17.598 3.045 10 A_DA10:DT13_B A 10 ? B 13 ? 20 1 1 A DG 11 1_555 B DC 1 1_555 0.076 -0.133 -0.075 -15.247 -18.632 -1.629 11 A_DG11:DC12_B A 11 ? B 12 ? 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 11 1_555 A DC 2 1_555 B DG 10 1_555 -0.192 -0.321 3.297 1.521 2.681 36.246 -0.889 0.521 3.255 4.300 -2.439 36.373 1 AA_DG1DC2:DG21DC22_BB A 1 ? B 22 ? A 2 ? B 21 ? 1 A DC 2 1_555 B DG 10 1_555 A DA 3 1_555 B DT 9 1_555 -0.723 -0.859 3.289 -4.335 16.413 35.565 -3.170 0.575 2.718 25.180 6.650 39.290 2 AA_DC2DA3:DT20DG21_BB A 2 ? B 21 ? A 3 ? B 20 ? 1 A DA 3 1_555 B DT 9 1_555 A DT 4 1_555 B DA 8 1_555 0.656 -1.354 3.401 -1.857 -1.324 32.018 -2.202 -1.534 3.410 -2.397 3.361 32.097 3 AA_DA3DT4:DA19DT20_BB A 3 ? B 20 ? A 4 ? B 19 ? 1 A DT 4 1_555 B DA 8 1_555 A DA 5 1_555 B DT 7 1_555 -0.192 -1.035 2.574 5.915 17.166 28.784 -3.708 0.996 1.647 30.950 -10.664 33.930 4 AA_DT4DA5:DT18DA19_BB A 4 ? B 19 ? A 5 ? B 18 ? 1 A DA 5 1_555 B DT 7 1_555 A DT 6 1_555 B DA 6 1_555 -0.600 -0.725 3.014 -3.851 6.091 26.501 -2.895 0.400 2.837 12.985 8.209 27.446 5 AA_DA5DT6:DA17DT18_BB A 5 ? B 18 ? A 6 ? B 17 ? 1 A DT 6 1_555 B DA 6 1_555 A DG 7 1_555 B DC 5 1_555 0.646 -0.666 2.896 -2.584 15.552 29.689 -3.285 -1.473 2.222 28.004 4.653 33.532 6 AA_DT6DG7:DC16DA17_BB A 6 ? B 17 ? A 7 ? B 16 ? 1 A DG 7 1_555 B DC 5 1_555 A DA 8 1_555 B DT 4 1_555 -0.006 -0.544 3.462 4.422 9.152 38.520 -1.906 0.544 3.235 13.586 -6.565 39.789 7 AA_DG7DA8:DT15DC16_BB A 7 ? B 16 ? A 8 ? B 15 ? 1 A DA 8 1_555 B DT 4 1_555 A DT 9 1_555 B DA 3 1_555 0.568 -0.857 2.982 -0.434 -2.210 32.288 -1.178 -1.089 3.025 -3.969 0.779 32.365 8 AA_DA8DT9:DA14DT15_BB A 8 ? B 15 ? A 9 ? B 14 ? 1 A DT 9 1_555 B DA 3 1_555 A DA 10 1_555 B DT 2 1_555 0.072 -1.313 3.258 8.397 19.250 33.327 -4.034 0.800 2.172 30.136 -13.145 39.233 9 AA_DT9DA10:DT13DA14_BB A 9 ? B 14 ? A 10 ? B 13 ? 1 A DA 10 1_555 B DT 2 1_555 A DG 11 1_555 B DC 1 1_555 -0.168 -0.469 3.071 -4.997 7.889 29.271 -2.322 -0.592 2.841 15.133 9.586 30.694 10 AA_DA10DG11:DC12DT13_BB A 10 ? B 13 ? A 11 ? B 12 ? #