data_1N4B # _entry.id 1N4B # _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 1N4B RCSB RCSB017501 WWPDB D_1000017501 # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1N4B _pdbx_database_status.recvd_initial_deposition_date 2002-10-30 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _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 'Webba da Silva, M.' 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 ;Solution Structure of a DNA Duplex Containing Mispair-Aligned N4C-Ethyl-N4C Interstrand Cross-Linked Cytosines ; _citation.journal_abbrev Biochemistry _citation.journal_volume 41 _citation.page_first 15181 _citation.page_last 15188 _citation.year 2002 _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 12484755 _citation.pdbx_database_id_DOI 10.1021/bi026368l # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Webba da Silva, M.' 1 primary 'Noronha, A.M.' 2 primary 'Noll, D.M.' 3 primary 'Miller, P.S.' 4 primary 'Colvin, O.M.' 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 "5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'" 3333.198 1 ? ? ? 'Interstrand Cross-Linked DNA' 2 polymer syn "5'-D(*CP*GP*AP*AP*AP*D00*TP*TP*TP*CP*G)-3'" 3361.251 1 ? ? ? 'Interstrand Cross-Linked DNA' # 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)(DG)(DA)(DA)(DA)(DC)(DT)(DT)(DT)(DC)(DG)' CGAAACTTTCG A ? 2 polydeoxyribonucleotide no yes '(DC)(DG)(DA)(DA)(DA)(D00)(DT)(DT)(DT)(DC)(DG)' CGAAAXTTTCG 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 DC 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 D00 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 1N4B 1N4B ? ? ? 2 2 PDB 1N4B 1N4B ? ? ? # 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 1N4B A 1 ? 11 ? 1N4B 1 ? 11 ? 1 11 2 2 1N4B B 1 ? 11 ? 1N4B 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 D00 'DNA linking' n ;2'-deoxy-N-ethylcytidine 5'-(dihydrogen phosphate) ; ? 'C11 H18 N3 O7 P' 335.250 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' 3 1 1 DQF-COSY 4 2 1 '2D NOESY' # 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 1 293 normal 7.4 '100 mM NaCl' ? K 2 273 normal 7.4 '100 mM NaCl' ? K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents ;The synthesis by solid phase methods of DNA duplexes that contain an N4-C-ethyl-N4C interstrand cross-link has been described [Biochemistry,41(2002)760-771]. 2 mM single strand concentration in 0.3 mL containing 10 mM sodium phosphate (pH 7.4) and 100 mM NaCl. ; _pdbx_nmr_sample_details.solvent_system 'both 1H2O (95%) and 2H2O (5%), and 99.9 % 2H2O.' # 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 3 ? Varian INOVA 500 # _pdbx_nmr_refine.entry_id 1N4B _pdbx_nmr_refine.method ;distance geometry simulated annealing molecular dynamics ; _pdbx_nmr_refine.details ;A total of 449 restraints were used 243 non-exchangeable 53 exchangeable 44 hydrogen bond 109 dihedral angle ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1N4B _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'the structure submitted is the lowest energy structure of a an ensemble of selected ten structures' _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 1N4B _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'closest to the average,lowest energy' # _pdbx_nmr_software.name X-PLOR _pdbx_nmr_software.version 3.8 _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors 'Brunger, A.T.' _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 1N4B _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 x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _struct.entry_id 1N4B _struct.title 'Solution Structure of the undecamer CGAAAC*TTTCG' _struct.pdbx_descriptor "5'-D(*CP*GP*AP*AP*AP*CP*TP*TP*TP*CP*G)-3'" _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1N4B _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'interstrand cross-link, alkylated DNA, modified cytosine, alkylated cytosine, 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 ? ? B DA 5 "O3'" ? ? ? 1_555 B D00 6 P ? ? B DA 5 B D00 6 1_555 ? ? ? ? ? ? ? 1.614 ? covale2 covale ? ? B D00 6 "O3'" ? ? ? 1_555 B DT 7 P ? ? B D00 6 B DT 7 1_555 ? ? ? ? ? ? ? 1.601 ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 2 B DC 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DA 3 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 3 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DA 3 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 3 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 4 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 4 B DT 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? hydrog9 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O2 ? ? A DA 5 B DT 8 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? hydrog10 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 8 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 8 B DA 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DT 8 O2 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 5 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? hydrog13 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 9 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 9 B DA 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 9 B DA 4 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? hydrog16 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 10 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1N4B _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 1N4B _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 DC 6 6 6 DC CYZ 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 D00 6 6 6 D00 CYZ 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 B _pdbx_struct_mod_residue.label_comp_id D00 _pdbx_struct_mod_residue.label_seq_id 6 _pdbx_struct_mod_residue.auth_asym_id B _pdbx_struct_mod_residue.auth_comp_id D00 _pdbx_struct_mod_residue.auth_seq_id 6 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DC _pdbx_struct_mod_residue.details ? # _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 2003-11-04 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2014-06-25 # _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' # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 N4 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 DC _pdbx_validate_close_contact.auth_seq_id_1 6 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 ? _pdbx_validate_close_contact.auth_atom_id_2 C10 _pdbx_validate_close_contact.auth_asym_id_2 B _pdbx_validate_close_contact.auth_comp_id_2 D00 _pdbx_validate_close_contact.auth_seq_id_2 6 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 1.47 # 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 ? ? N1 A DC 1 ? ? 112.20 108.30 3.90 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? "C2'" A DG 2 ? ? 100.59 105.90 -5.31 0.80 N 3 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 103.26 108.00 -4.74 0.70 N 4 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 111.70 108.30 3.40 0.30 N 5 1 "C1'" A DA 4 ? ? "O4'" A DA 4 ? ? "C4'" A DA 4 ? ? 102.29 110.10 -7.81 1.00 N 6 1 "C4'" A DA 4 ? ? "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? 97.92 102.20 -4.28 0.70 N 7 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? "C2'" A DA 4 ? ? 94.97 105.90 -10.93 0.80 N 8 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? "C2'" A DC 6 ? ? 94.80 105.90 -11.10 0.80 N 9 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 100.87 108.00 -7.13 0.70 N 10 1 C2 A DC 6 ? ? N3 A DC 6 ? ? C4 A DC 6 ? ? 124.47 119.90 4.57 0.50 N 11 1 N3 A DC 6 ? ? C4 A DC 6 ? ? C5 A DC 6 ? ? 116.60 121.90 -5.30 0.40 N 12 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? "C2'" A DT 7 ? ? 96.47 105.90 -9.43 0.80 N 13 1 C4 A DT 7 ? ? C5 A DT 7 ? ? C6 A DT 7 ? ? 121.98 118.00 3.98 0.60 N 14 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 118.21 122.90 -4.69 0.60 N 15 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? "C2'" A DT 8 ? ? 96.13 105.90 -9.77 0.80 N 16 1 "C5'" A DT 9 ? ? "C4'" A DT 9 ? ? "O4'" A DT 9 ? ? 117.73 109.80 7.93 1.10 N 17 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? "C2'" A DT 9 ? ? 95.26 105.90 -10.64 0.80 N 18 1 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.10 122.90 -3.80 0.60 N 19 1 "C1'" A DC 10 ? ? "O4'" A DC 10 ? ? "C4'" A DC 10 ? ? 103.94 110.10 -6.16 1.00 N 20 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? "C2'" A DC 10 ? ? 92.87 105.90 -13.03 0.80 N 21 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 111.70 108.30 3.40 0.30 N 22 1 "O4'" A DG 11 ? ? "C4'" A DG 11 ? ? "C3'" A DG 11 ? ? 101.88 104.50 -2.62 0.40 N 23 1 "O4'" B DC 1 ? ? "C1'" B DC 1 ? ? N1 B DC 1 ? ? 112.18 108.30 3.88 0.30 N 24 1 "O4'" B DG 2 ? ? "C1'" B DG 2 ? ? "C2'" B DG 2 ? ? 100.17 105.90 -5.73 0.80 N 25 1 "O4'" B DG 2 ? ? "C1'" B DG 2 ? ? N9 B DG 2 ? ? 103.12 108.00 -4.88 0.70 N 26 1 "C4'" B DA 3 ? ? "C3'" B DA 3 ? ? "C2'" B DA 3 ? ? 97.76 102.20 -4.44 0.70 N 27 1 "O4'" B DA 3 ? ? "C1'" B DA 3 ? ? N9 B DA 3 ? ? 111.18 108.30 2.88 0.30 N 28 1 "C1'" B DA 4 ? ? "O4'" B DA 4 ? ? "C4'" B DA 4 ? ? 102.77 110.10 -7.33 1.00 N 29 1 "O4'" B DA 4 ? ? "C1'" B DA 4 ? ? "C2'" B DA 4 ? ? 94.47 105.90 -11.43 0.80 N 30 1 "O4'" B DT 7 ? ? "C1'" B DT 7 ? ? "C2'" B DT 7 ? ? 96.14 105.90 -9.76 0.80 N 31 1 C4 B DT 7 ? ? C5 B DT 7 ? ? C6 B DT 7 ? ? 121.88 118.00 3.88 0.60 N 32 1 C6 B DT 7 ? ? C5 B DT 7 ? ? C7 B DT 7 ? ? 118.52 122.90 -4.38 0.60 N 33 1 "O4'" B DT 8 ? ? "C1'" B DT 8 ? ? "C2'" B DT 8 ? ? 95.46 105.90 -10.44 0.80 N 34 1 C4 B DT 8 ? ? C5 B DT 8 ? ? C6 B DT 8 ? ? 121.62 118.00 3.62 0.60 N 35 1 "C5'" B DT 9 ? ? "C4'" B DT 9 ? ? "O4'" B DT 9 ? ? 117.39 109.80 7.59 1.10 N 36 1 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? "C2'" B DT 9 ? ? 94.85 105.90 -11.05 0.80 N 37 1 C6 B DT 9 ? ? C5 B DT 9 ? ? C7 B DT 9 ? ? 119.12 122.90 -3.78 0.60 N 38 1 "C4'" B DC 10 ? ? "C3'" B DC 10 ? ? "O3'" B DC 10 ? ? 124.40 112.30 12.10 2.00 N 39 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? "C2'" B DC 10 ? ? 92.57 105.90 -13.33 0.80 N 40 1 "O4'" B DC 10 ? ? "C1'" B DC 10 ? ? N1 B DC 10 ? ? 111.49 108.30 3.19 0.30 N 41 1 "O4'" B DG 11 ? ? "C4'" B DG 11 ? ? "C3'" B DG 11 ? ? 101.41 104.50 -3.09 0.40 N # _pdbx_validate_planes.id 1 _pdbx_validate_planes.PDB_model_num 1 _pdbx_validate_planes.auth_comp_id DC _pdbx_validate_planes.auth_asym_id A _pdbx_validate_planes.auth_seq_id 6 _pdbx_validate_planes.PDB_ins_code ? _pdbx_validate_planes.label_alt_id ? _pdbx_validate_planes.rmsd 0.109 _pdbx_validate_planes.type 'SIDE CHAIN' # _pdbx_unobs_or_zero_occ_atoms.id 1 _pdbx_unobs_or_zero_occ_atoms.PDB_model_num 1 _pdbx_unobs_or_zero_occ_atoms.polymer_flag Y _pdbx_unobs_or_zero_occ_atoms.occupancy_flag 1 _pdbx_unobs_or_zero_occ_atoms.auth_asym_id B _pdbx_unobs_or_zero_occ_atoms.auth_comp_id D00 _pdbx_unobs_or_zero_occ_atoms.auth_seq_id 6 _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code ? _pdbx_unobs_or_zero_occ_atoms.auth_atom_id C2 _pdbx_unobs_or_zero_occ_atoms.label_alt_id ? _pdbx_unobs_or_zero_occ_atoms.label_asym_id B _pdbx_unobs_or_zero_occ_atoms.label_comp_id D00 _pdbx_unobs_or_zero_occ_atoms.label_seq_id 6 _pdbx_unobs_or_zero_occ_atoms.label_atom_id C2 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1N4B 'b-form double helix' 1N4B 'triple 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 2 1_555 B DC 10 1_555 -0.634 -0.408 -0.512 -2.253 3.774 -3.265 1 A_DG2:DC10_B A 2 ? B 10 ? 19 1 1 A DA 3 1_555 B DT 9 1_555 0.121 -0.135 -0.434 20.467 -1.950 3.706 2 A_DA3:DT9_B A 3 ? B 9 ? 20 1 1 A DA 4 1_555 B DT 8 1_555 -0.196 -0.377 -0.382 34.624 -12.747 2.568 3 A_DA4:DT8_B A 4 ? B 8 ? 20 1 1 A DT 8 1_555 B DA 4 1_555 0.203 -0.364 -0.388 -34.711 -12.734 2.579 4 A_DT8:DA4_B A 8 ? B 4 ? 20 1 1 A DT 9 1_555 B DA 3 1_555 -0.110 -0.125 -0.443 -20.440 -1.858 3.830 5 A_DT9:DA3_B A 9 ? B 3 ? 20 1 1 A DC 10 1_555 B DG 2 1_555 0.653 -0.407 -0.519 2.413 3.867 -3.247 6 A_DC10:DG2_B A 10 ? B 2 ? 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 2 1_555 B DC 10 1_555 A DA 3 1_555 B DT 9 1_555 -0.256 0.225 2.676 0.229 2.598 36.192 0.064 0.437 2.684 4.176 -0.367 36.282 1 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 -0.343 0.108 2.798 -1.405 2.514 28.352 -0.275 0.421 2.810 5.116 2.859 28.495 2 AA_DA3DA4:DT8DT9_BB A 3 ? B 9 ? A 4 ? B 8 ? 1 A DT 8 1_555 B DA 4 1_555 A DT 9 1_555 B DA 3 1_555 0.342 0.111 2.795 1.436 2.482 28.301 -0.263 -0.414 2.807 5.060 -2.928 28.443 3 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 0.252 0.228 2.674 -0.260 2.676 36.240 0.059 -0.434 2.681 4.294 0.418 36.337 4 AA_DT9DC10:DG2DA3_BB A 9 ? B 3 ? A 10 ? B 2 ? #