data_1S37 # _entry.id 1S37 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1S37 RCSB RCSB021309 WWPDB D_1000021309 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1N74 'DNA interstrand crosslink' unspecified PDB 1N4B 'DNA interstrand crosslink' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1S37 _pdbx_database_status.recvd_initial_deposition_date 2004-01-12 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'da Silva, M.W.' 1 'Noronha, A.M.' 2 'Noll, D.M.' 3 'Miller, P.S.' 4 'Colvin, O.M.' 5 'Gamcsik, M.P.' 6 # _citation.id primary _citation.title 'Accommodation of mispair aligned N3T-ethyl-N3T DNA interstrand cross link.' _citation.journal_abbrev Biochemistry _citation.journal_volume 43 _citation.page_first 12549 _citation.page_last 12554 _citation.year 2004 _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 15449944 _citation.pdbx_database_id_DOI 10.1021/bi0486435 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'da Silva, M.W.' 1 primary 'Wilds, C.J.' 2 primary 'Noronha, A.M.' 3 primary 'Colvin, O.M.' 4 primary 'Miller, P.S.' 5 primary 'Gamcsik, M.P.' 6 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*GP*AP*AP*AP*(TTM)P*TP*TP*TP*CP*G)-3') ; 3376.263 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3') ; 3348.209 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 yes '(DC)(DG)(DA)(DA)(DA)(TTM)(DT)(DT)(DT)(DC)(DG)' CGAAATTTTCG A ? 2 polydeoxyribonucleotide no no '(DC)(DG)(DA)(DA)(DA)(DT)(DT)(DT)(DT)(DC)(DG)' CGAAATTTTCG 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 DG n 1 3 DA n 1 4 DA n 1 5 DA n 1 6 TTM n 1 7 DT n 1 8 DT n 1 9 DT n 1 10 DC n 1 11 DG n 2 1 DC n 2 2 DG n 2 3 DA n 2 4 DA n 2 5 DA n 2 6 DT n 2 7 DT n 2 8 DT n 2 9 DT n 2 10 DC n 2 11 DG 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_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 1S37 1S37 ? ? ? 2 2 PDB 1S37 1S37 ? ? ? # 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 1S37 A 1 ? 11 ? 1S37 1 ? 11 ? 1 11 2 2 1S37 B 1 ? 11 ? 1S37 1 ? 11 ? 1 11 # 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 TTM 'DNA linking' n "N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE" ? 'C12 H19 N2 O8 P' 350.262 # 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' 3 1 1 DQF-COSY # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.temperature_units 1 273 normal 7.4 '0.1 mM NaCl' ? K 2 298 normal 7.4 '0.1 mM NaCl' ? K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '100 mM NaCl, pH 7.4 adjusted with phosphate buffer' _pdbx_nmr_sample_details.solvent_system 'H2O, 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 INOVA 800 2 ? Varian INOVA 600 # _pdbx_nmr_refine.entry_id 1S37 _pdbx_nmr_refine.method 'distance geometry, simulated annealing, molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1S37 _pdbx_nmr_details.text 'Structure Determined using standard NMR experiments.' # _pdbx_nmr_ensemble.entry_id 1S37 _pdbx_nmr_ensemble.conformers_calculated_total_number 8 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria '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 1S37 _pdbx_nmr_representative.conformer_id 8 _pdbx_nmr_representative.selection_criteria 'minimized average structure' # loop_ _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.classification _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal FELIX 2000 'data analysis' ? 1 X-PLOR 3.2 refinement 'A.T. Brunger' 2 # _exptl.entry_id 1S37 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? _exptl_crystal.density_Matthews ? # _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 x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1S37 _struct.title 'Accomodation of Mispair-Aligned N3T-Ethyl-N3T DNA Interstrand Crosslink' _struct.pdbx_descriptor "5'-D(*CP*GP*AP*AP*AP*TP*TP*TP*TP*CP*G)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'minimized average' # _struct_keywords.entry_id 1S37 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'interstrand crosslink, DNA interstrand cross-link, 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 _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 covale1 covale ? ? A DA 5 "O3'" ? ? ? 1_555 A TTM 6 P ? ? A DA 5 A TTM 6 1_555 ? ? ? ? ? ? ? 1.593 ? covale2 covale ? ? A TTM 6 "O3'" ? ? ? 1_555 A DT 7 P ? ? A TTM 6 A DT 7 1_555 ? ? ? ? ? ? ? 1.594 ? covale3 covale ? ? A TTM 6 C2Q ? ? ? 1_555 B DT 6 N3 ? ? A TTM 6 B DT 6 1_555 ? ? ? ? ? ? ? 1.479 ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 1 B DG 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 3 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 3 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 4 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 4 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 5 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 5 B DT 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 7 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 7 B DA 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 8 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 8 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 9 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 9 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog21 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog22 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog23 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog24 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 11 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1S37 _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 1S37 _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 DG 2 2 2 DG GUA A . n A 1 3 DA 3 3 3 DA ADE A . n A 1 4 DA 4 4 4 DA ADE A . n A 1 5 DA 5 5 5 DA ADE A . n A 1 6 TTM 6 6 6 TTM THZ A . n A 1 7 DT 7 7 7 DT THY A . n A 1 8 DT 8 8 8 DT THY A . n A 1 9 DT 9 9 9 DT THY A . n A 1 10 DC 10 10 10 DC CYT A . n A 1 11 DG 11 11 11 DG GUA A . n B 2 1 DC 1 1 1 DC CYT B . n B 2 2 DG 2 2 2 DG GUA B . n B 2 3 DA 3 3 3 DA ADE B . n B 2 4 DA 4 4 4 DA ADE B . n B 2 5 DA 5 5 5 DA ADE B . n B 2 6 DT 6 6 6 DT THZ B . n B 2 7 DT 7 7 7 DT THY B . n B 2 8 DT 8 8 8 DT THY B . n B 2 9 DT 9 9 9 DT THY B . n B 2 10 DC 10 10 10 DC CYT B . n B 2 11 DG 11 11 11 DG GUA B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id TTM _pdbx_struct_mod_residue.label_seq_id 6 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id TTM _pdbx_struct_mod_residue.auth_seq_id 6 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DT _pdbx_struct_mod_residue.details "N3-ETHYL-THYMIDINE-5'-MONOPHOSPHATE" # _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 2005-01-25 2 'Structure model' 1 1 2008-04-29 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-07-30 # _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 ? # 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' 'Structure summary' # 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 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.46 105.90 -5.44 0.80 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.38 108.30 6.08 0.30 N 3 1 "C3'" A DG 2 ? ? "C2'" A DG 2 ? ? "C1'" A DG 2 ? ? 94.70 102.40 -7.70 0.80 N 4 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? "C2'" A DG 2 ? ? 100.64 105.90 -5.26 0.80 N 5 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? "C2'" A DA 3 ? ? 98.01 105.90 -7.89 0.80 N 6 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 110.92 108.30 2.62 0.30 N 7 1 C6 A DA 3 ? ? N1 A DA 3 ? ? C2 A DA 3 ? ? 122.55 118.60 3.95 0.60 N 8 1 N1 A DA 3 ? ? C6 A DA 3 ? ? N6 A DA 3 ? ? 122.75 118.60 4.15 0.60 N 9 1 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? "C1'" A DA 4 ? ? 97.20 102.40 -5.20 0.80 N 10 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 113.28 108.30 4.98 0.30 N 11 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 122.36 118.60 3.76 0.60 N 12 1 "C4'" A DA 5 ? ? "C3'" A DA 5 ? ? "C2'" A DA 5 ? ? 96.18 102.20 -6.02 0.70 N 13 1 N1 A DA 5 ? ? C6 A DA 5 ? ? N6 A DA 5 ? ? 122.41 118.60 3.81 0.60 N 14 1 "C3'" A DT 7 ? ? "C2'" A DT 7 ? ? "C1'" A DT 7 ? ? 97.07 102.40 -5.33 0.80 N 15 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 99.32 105.90 -6.58 0.80 N 16 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C6 A DT 7 ? ? 121.80 118.00 3.80 0.60 N 17 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 122.64 119.00 3.64 0.60 N 18 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 115.56 122.90 -7.34 0.60 N 19 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? "C2'" A DT 8 ? ? 100.97 105.90 -4.93 0.80 N 20 1 C4 A DT 8 ? ? C5 A DT 8 ? ? C6 A DT 8 ? ? 121.99 118.00 3.99 0.60 N 21 1 C6 A DT 8 ? ? C5 A DT 8 ? ? C7 A DT 8 ? ? 118.96 122.90 -3.94 0.60 N 22 1 "C1'" A DT 9 ? ? "O4'" A DT 9 ? ? "C4'" A DT 9 ? ? 103.99 110.10 -6.11 1.00 N 23 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? "C2'" A DT 9 ? ? 95.61 105.90 -10.29 0.80 N 24 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 111.72 108.30 3.42 0.30 N 25 1 C4 A DT 9 ? ? C5 A DT 9 ? ? C6 A DT 9 ? ? 121.70 118.00 3.70 0.60 N 26 1 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 116.00 122.90 -6.90 0.60 N 27 1 "C3'" A DC 10 ? ? "C2'" A DC 10 ? ? "C1'" A DC 10 ? ? 94.35 102.40 -8.05 0.80 N 28 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? "C2'" A DC 10 ? ? 100.76 105.90 -5.14 0.80 N 29 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 111.40 108.30 3.10 0.30 N 30 1 N1 A DC 10 ? ? C2 A DC 10 ? ? O2 A DC 10 ? ? 122.96 118.90 4.06 0.60 N 31 1 "O4'" A DG 11 ? ? "C4'" A DG 11 ? ? "C3'" A DG 11 ? ? 99.26 104.50 -5.24 0.40 N 32 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 111.62 108.30 3.32 0.30 N 33 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? "C2'" B DC 1 ? ? 100.22 105.90 -5.68 0.80 N 34 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 114.08 108.30 5.78 0.30 N 35 1 "C3'" B DG 2 ? ? "C2'" B DG 2 ? ? "C1'" B DG 2 ? ? 94.88 102.40 -7.52 0.80 N 36 1 "O4'" B DG 2 ? ? "C1'" B DG 2 ? ? "C2'" B DG 2 ? ? 100.40 105.90 -5.50 0.80 N 37 1 "O4'" B DA 3 ? ? "C1'" B DA 3 ? ? "C2'" B DA 3 ? ? 97.85 105.90 -8.05 0.80 N 38 1 "O4'" B DA 3 ? ? "C1'" B DA 3 ? ? N9 B DA 3 ? ? 110.95 108.30 2.65 0.30 N 39 1 C6 B DA 3 ? ? N1 B DA 3 ? ? C2 B DA 3 ? ? 122.47 118.60 3.87 0.60 N 40 1 N1 B DA 3 ? ? C6 B DA 3 ? ? N6 B DA 3 ? ? 122.82 118.60 4.22 0.60 N 41 1 "C3'" B DA 4 ? ? "C2'" B DA 4 ? ? "C1'" B DA 4 ? ? 96.96 102.40 -5.44 0.80 N 42 1 "O4'" B DA 4 ? ? "C1'" B DA 4 ? ? N9 B DA 4 ? ? 113.25 108.30 4.95 0.30 N 43 1 N1 B DA 4 ? ? C6 B DA 4 ? ? N6 B DA 4 ? ? 122.35 118.60 3.75 0.60 N 44 1 "C4'" B DA 5 ? ? "C3'" B DA 5 ? ? "C2'" B DA 5 ? ? 96.63 102.20 -5.57 0.70 N 45 1 N1 B DA 5 ? ? C6 B DA 5 ? ? N6 B DA 5 ? ? 122.43 118.60 3.83 0.60 N 46 1 C6 B DT 6 ? ? C5 B DT 6 ? ? C7 B DT 6 ? ? 116.46 122.90 -6.44 0.60 N 47 1 "C3'" B DT 7 ? ? "C2'" B DT 7 ? ? "C1'" B DT 7 ? ? 97.15 102.40 -5.25 0.80 N 48 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? "C2'" B DT 7 ? ? 98.72 105.90 -7.18 0.80 N 49 1 C4 B DT 7 ? ? C5 B DT 7 ? ? C6 B DT 7 ? ? 121.66 118.00 3.66 0.60 N 50 1 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 116.43 122.90 -6.47 0.60 N 51 1 "C3'" B DT 8 ? ? "C2'" B DT 8 ? ? "C1'" B DT 8 ? ? 97.57 102.40 -4.83 0.80 N 52 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? "C2'" B DT 8 ? ? 100.59 105.90 -5.31 0.80 N 53 1 C4 B DT 8 ? ? C5 B DT 8 ? ? C6 B DT 8 ? ? 121.96 118.00 3.96 0.60 N 54 1 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? "C2'" B DT 9 ? ? 95.50 105.90 -10.40 0.80 N 55 1 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 111.87 108.30 3.57 0.30 N 56 1 C4 B DT 9 ? ? C5 B DT 9 ? ? C6 B DT 9 ? ? 121.64 118.00 3.64 0.60 N 57 1 C6 B DT 9 ? ? C5 B DT 9 ? ? C7 B DT 9 ? ? 116.51 122.90 -6.39 0.60 N 58 1 "C3'" B DC 10 ? ? "C2'" B DC 10 ? ? "C1'" B DC 10 ? ? 94.42 102.40 -7.98 0.80 N 59 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? "C2'" B DC 10 ? ? 100.49 105.90 -5.41 0.80 N 60 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 111.50 108.30 3.20 0.30 N 61 1 N1 B DC 10 ? ? C2 B DC 10 ? ? O2 B DC 10 ? ? 122.93 118.90 4.03 0.60 N 62 1 "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? "C3'" B DG 11 ? ? 99.42 104.50 -5.08 0.40 N 63 1 "O4'" B DG 11 ? ? "C1'" B DG 11 ? ? N9 B DG 11 ? ? 111.64 108.30 3.34 0.30 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1S37 'double helix' 1S37 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 11 1_555 0.176 -0.268 -0.044 0.818 0.231 -1.656 1 A_DC1:DG11_B A 1 ? B 11 ? 19 1 1 A DG 2 1_555 B DC 10 1_555 -0.065 -0.163 0.006 0.050 -0.425 -3.573 2 A_DG2:DC10_B A 2 ? B 10 ? 19 1 1 A DA 3 1_555 B DT 9 1_555 -0.119 -0.251 0.100 0.344 1.008 1.635 3 A_DA3:DT9_B A 3 ? B 9 ? 20 1 1 A DA 4 1_555 B DT 8 1_555 0.054 -0.168 -0.214 -0.885 -2.269 -7.381 4 A_DA4:DT8_B A 4 ? B 8 ? 20 1 1 A DA 5 1_555 B DT 7 1_555 -0.160 -0.281 0.008 2.129 -2.360 -0.452 5 A_DA5:DT7_B A 5 ? B 7 ? 20 1 1 A DT 7 1_555 B DA 5 1_555 0.160 -0.284 0.018 -2.206 -2.328 -0.565 6 A_DT7:DA5_B A 7 ? B 5 ? 20 1 1 A DT 8 1_555 B DA 4 1_555 -0.054 -0.172 -0.228 1.109 -2.263 -7.456 7 A_DT8:DA4_B A 8 ? B 4 ? 20 1 1 A DT 9 1_555 B DA 3 1_555 0.119 -0.255 0.115 -0.616 0.965 1.593 8 A_DT9:DA3_B A 9 ? B 3 ? 20 1 1 A DC 10 1_555 B DG 2 1_555 0.061 -0.164 0.007 -0.127 -0.412 -3.681 9 A_DC10:DG2_B A 10 ? B 2 ? 19 1 1 A DG 11 1_555 B DC 1 1_555 -0.174 -0.268 -0.042 -0.796 0.250 -1.729 10 A_DG11:DC1_B A 11 ? B 1 ? 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 11 1_555 A DG 2 1_555 B DC 10 1_555 0.154 0.333 3.026 -0.640 0.699 42.605 0.393 -0.272 3.028 0.962 0.881 42.615 1 AA_DC1DG2:DC10DG11_BB A 1 ? B 11 ? A 2 ? B 10 ? 1 A DG 2 1_555 B DC 10 1_555 A DA 3 1_555 B DT 9 1_555 0.720 -0.712 3.119 0.653 7.352 32.385 -2.396 -1.157 2.905 12.972 -1.153 33.193 2 AA_DG2DA3:DT9DC10_BB A 2 ? B 10 ? A 3 ? B 9 ? 1 A DA 3 1_555 B DT 9 1_555 A DA 4 1_555 B DT 8 1_555 -1.371 -0.187 3.326 -0.430 5.088 36.482 -0.997 2.112 3.287 8.078 0.683 36.826 3 AA_DA3DA4:DT8DT9_BB A 3 ? B 9 ? A 4 ? B 8 ? 1 A DA 4 1_555 B DT 8 1_555 A DA 5 1_555 B DT 7 1_555 -0.234 0.026 3.043 -2.140 -12.363 43.160 1.081 0.126 2.937 -16.397 2.838 44.863 4 AA_DA4DA5:DT7DT8_BB A 4 ? B 8 ? A 5 ? B 7 ? 1 A DA 5 1_555 B DT 7 1_555 A DT 7 1_555 B DA 5 1_555 0.002 -0.807 6.149 -0.084 2.463 71.026 -0.853 -0.007 6.122 2.119 0.072 71.063 5 AA_DA5DT7:DA5DT7_BB A 5 ? B 7 ? A 7 ? B 5 ? 1 A DT 7 1_555 B DA 5 1_555 A DT 8 1_555 B DA 4 1_555 0.235 0.025 3.032 2.334 -12.411 43.165 1.079 -0.111 2.926 -16.453 -3.094 44.890 6 AA_DT7DT8:DA4DA5_BB A 7 ? B 5 ? A 8 ? B 4 ? 1 A DT 8 1_555 B DA 4 1_555 A DT 9 1_555 B DA 3 1_555 1.375 -0.189 3.342 0.259 5.158 36.512 -1.011 -2.138 3.295 8.182 -0.411 36.863 7 AA_DT8DT9:DA3DA4_BB A 8 ? B 4 ? A 9 ? B 3 ? 1 A DT 9 1_555 B DA 3 1_555 A DC 10 1_555 B DG 2 1_555 -0.723 -0.715 3.111 -0.588 7.293 32.359 -2.394 1.175 2.898 12.882 1.038 33.154 8 AA_DT9DC10:DG2DA3_BB A 9 ? B 3 ? A 10 ? B 2 ? 1 A DC 10 1_555 B DG 2 1_555 A DG 11 1_555 B DC 1 1_555 -0.154 0.331 3.023 0.635 0.659 42.675 0.393 0.270 3.025 0.905 -0.872 42.684 9 AA_DC10DG11:DC1DG2_BB A 10 ? B 2 ? A 11 ? B 1 ? #