data_1AGO # _entry.id 1AGO # _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 1AGO pdb_00001ago 10.2210/pdb1ago/pdb WWPDB D_1000170793 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1AGK 'MINIMIZED AVERAGE STRUCTURE' unspecified PDB 1AGZ 'MINIMIZED AVERAGE STRUCTURE' unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1AGO _pdbx_database_status.recvd_initial_deposition_date 1997-03-25 _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 'Feng, B.' 1 'Stone, M.P.' 2 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Major groove (S)-alpha-(N6-adenyl)styrene oxide adducts in an oligodeoxynucleotide containing the human N-ras codon 61 sequence: conformations of the S(61,2) and S(61,3) sequence isomers from 1H NMR. ; Biochemistry 35 7316 7329 1996 BICHAW US 0006-2960 0033 ? 8652508 10.1021/bi952526f 1 ;Solution Structure of an Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence Refined from 1H NMR Using Molecular Dynamics Restrained by Nuclear Overhauser Effects ; Chem.Res.Toxicol. 8 821 ? 1995 CRTOEC US 0893-228X 2140 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Feng, B.' 1 ? primary 'Voehler, M.' 2 ? primary 'Zhou, L.' 3 ? primary 'Passarelli, M.' 4 ? primary 'Harris, C.M.' 5 ? primary 'Harris, T.M.' 6 ? primary 'Stone, M.P.' 7 ? 1 'Feng, B.' 8 ? 1 'Stone, M.P.' 9 ? # _cell.entry_id 1AGO _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 1AGO _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 ;DNA (5'-D(*CP*GP*GP*AP*CP*AP*YP*GP*AP*AP*G)-3') ; 3536.411 1 ? ? ? '(S)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 DNA ADDUCT' 2 polymer syn ;DNA (5'-D(*CP*TP*TP*CP*TP*TP*GP*TP*CP*CP*G)-3') ; 3291.145 1 ? ? ? '(S)-(N6-ADENYL)-STYRENE OXIDE-RAS61-3 DNA ADDUCT' # 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)(DG)(DA)(DC)(DA)(Y)(DG)(DA)(DA)(DG)' CGGACAAGAAG A ? 2 polydeoxyribonucleotide no no '(DC)(DT)(DT)(DC)(DT)(DT)(DG)(DT)(DC)(DC)(DG)' CTTCTTGTCCG 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 DG n 1 4 DA n 1 5 DC n 1 6 DA n 1 7 Y n 1 8 DG n 1 9 DA n 1 10 DA n 1 11 DG n 2 1 DC n 2 2 DT n 2 3 DT n 2 4 DC n 2 5 DT n 2 6 DT n 2 7 DG n 2 8 DT n 2 9 DC 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_db_isoform _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin 1 1 PDB 1AGO 1AGO ? ? ? 2 2 PDB 1AGO 1AGO ? ? ? # 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 1AGO A 1 ? 11 ? 1AGO 1 ? 11 ? 1 11 2 2 1AGO B 1 ? 11 ? 1AGO 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 Y 'DNA linking' n ;2'-DEOXY-N6-(S)STYRENE OXIDE ADENOSINE MONOPHOSPHATE ; ? 'C18 H22 N5 O7 P' 451.370 # 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 2QF-COSY 1 3 1 'AND TOCSY' 1 4 1 ': NOESY' 1 5 1 2QF-COSY 1 6 1 'AND(DO' 1 7 1 "05'-D" 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 293 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 6.9 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AMX500 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 500 # _pdbx_nmr_refine.entry_id 1AGO _pdbx_nmr_refine.method 'NOE-RESTRAINED MOLECULAR DYNAMICS/SIMULATED ANNEALING' _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1AGO _pdbx_nmr_ensemble.conformers_calculated_total_number 1 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA.' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' Felix ? ? 2 'structure solution' X-PLOR ? ? 3 'structure solution' MARDIGRAS ? ? 4 'structure solution' CORMA ? ? 5 # _exptl.entry_id 1AGO _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1AGO _struct.title ;THE SOLUTION NMR STRUCTURE OF AN (S)-A-(N6-ADENYL)-STYRENE OXIDE-RAS61 OLIGODEOXYNUCLEOTIDE MODIFIED AT THE THIRD POSITION OF THE CODON 61 REGION, MINIMIZED AVERAGE STRUCTURE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1AGO _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;DNA DUPLEX, B-DNA, HUMAN N-RAS GENE, CODON 61 SEQUENCE, S-STYRENE OXIDE ADDUCT, N6-ADENINE ADDUCT, MAJOR GROOVE ADDUCT, DEOXYRIBONUCLEIC ACID, 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 covale1 covale both ? A DA 6 "O3'" ? ? ? 1_555 A Y 7 P ? ? A DA 6 A Y 7 1_555 ? ? ? ? ? ? ? 1.626 ? ? covale2 covale both ? A Y 7 "O3'" ? ? ? 1_555 A DG 8 P ? ? A Y 7 A DG 8 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 11 N1 ? ? A DC 1 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 11 O6 ? ? A DC 1 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 11 N2 ? ? A DC 1 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 2 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 2 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 2 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 3 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 3 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 3 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 4 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 4 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 5 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 5 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 5 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 6 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A Y 7 N1 ? ? ? 1_555 B DT 5 N3 ? ? A Y 7 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A Y 7 N6 ? ? ? 1_555 B DT 5 O4 ? ? A Y 7 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 8 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 8 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 8 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 8 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 8 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 8 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DA 9 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 9 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DA 9 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 9 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DA 10 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 10 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DA 10 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 10 B DT 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 11 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1AGO _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 1AGO _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 C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 Y 7 7 7 Y Y A . n A 1 8 DG 8 8 8 DG G A . n A 1 9 DA 9 9 9 DA A 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 DT 3 14 14 DT T B . n B 2 4 DC 4 15 15 DC C B . n B 2 5 DT 5 16 16 DT T B . n B 2 6 DT 6 17 17 DT T B . n B 2 7 DG 7 18 18 DG G B . n B 2 8 DT 8 19 19 DT T B . n B 2 9 DC 9 20 20 DC C B . n B 2 10 DC 10 21 21 DC C B . n B 2 11 DG 11 22 22 DG G B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id Y _pdbx_struct_mod_residue.label_seq_id 7 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id Y _pdbx_struct_mod_residue.auth_seq_id 7 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DA _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 1997-08-20 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2022-02-16 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' Other 7 4 'Structure model' 'Polymer sequence' # 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' entity_poly 3 4 'Structure model' pdbx_database_status 4 4 'Structure model' pdbx_nmr_software 5 4 'Structure model' pdbx_struct_assembly 6 4 'Structure model' pdbx_struct_oper_list 7 4 'Structure model' struct_conn # 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' '_entity_poly.pdbx_seq_one_letter_code' 4 4 'Structure model' '_entity_poly.pdbx_seq_one_letter_code_can' 5 4 'Structure model' '_pdbx_database_status.process_site' 6 4 'Structure model' '_pdbx_nmr_software.name' 7 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 8 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 11 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 12 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 13 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 15 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 16 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 17 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 # 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 ? ? 110.77 108.30 2.47 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 110.93 108.30 2.63 0.30 N 3 1 N7 A DG 2 ? ? C8 A DG 2 ? ? N9 A DG 2 ? ? 117.59 113.10 4.49 0.50 N 4 1 C8 A DG 2 ? ? N9 A DG 2 ? ? C4 A DG 2 ? ? 103.66 106.40 -2.74 0.40 N 5 1 "O4'" A DG 3 ? ? "C1'" A DG 3 ? ? N9 A DG 3 ? ? 111.09 108.30 2.79 0.30 N 6 1 N7 A DG 3 ? ? C8 A DG 3 ? ? N9 A DG 3 ? ? 117.64 113.10 4.54 0.50 N 7 1 C8 A DG 3 ? ? N9 A DG 3 ? ? C4 A DG 3 ? ? 103.65 106.40 -2.75 0.40 N 8 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.33 108.30 3.03 0.30 N 9 1 N7 A DA 4 ? ? C8 A DA 4 ? ? N9 A DA 4 ? ? 117.43 113.80 3.63 0.50 N 10 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.69 108.30 3.39 0.30 N 11 1 "O3'" A DC 5 ? ? P A DA 6 ? ? "O5'" A DA 6 ? ? 67.09 104.00 -36.91 1.90 Y 12 1 "O3'" A DC 5 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 89.35 105.20 -15.85 2.20 Y 13 1 "O3'" A DC 5 ? ? P A DA 6 ? ? OP1 A DA 6 ? ? 136.00 110.50 25.50 1.10 Y 14 1 OP1 A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 102.27 119.60 -17.33 1.50 N 15 1 "O5'" A DA 6 ? ? P A DA 6 ? ? OP1 A DA 6 ? ? 72.31 105.70 -33.39 0.90 N 16 1 "O5'" A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 127.09 110.70 16.39 1.20 N 17 1 N7 A DA 6 ? ? C8 A DA 6 ? ? N9 A DA 6 ? ? 117.63 113.80 3.83 0.50 N 18 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.19 108.30 2.89 0.30 N 19 1 N7 A DG 8 ? ? C8 A DG 8 ? ? N9 A DG 8 ? ? 117.57 113.10 4.47 0.50 N 20 1 C8 A DG 8 ? ? N9 A DG 8 ? ? C4 A DG 8 ? ? 103.55 106.40 -2.85 0.40 N 21 1 "O4'" A DA 9 ? ? "C1'" A DA 9 ? ? N9 A DA 9 ? ? 110.55 108.30 2.25 0.30 N 22 1 N7 A DA 9 ? ? C8 A DA 9 ? ? N9 A DA 9 ? ? 117.46 113.80 3.66 0.50 N 23 1 "O4'" A DA 10 ? ? "C1'" A DA 10 ? ? N9 A DA 10 ? ? 110.64 108.30 2.34 0.30 N 24 1 N7 A DA 10 ? ? C8 A DA 10 ? ? N9 A DA 10 ? ? 117.47 113.80 3.67 0.50 N 25 1 C8 A DA 10 ? ? N9 A DA 10 ? ? C4 A DA 10 ? ? 103.27 105.80 -2.53 0.40 N 26 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 110.52 108.30 2.22 0.30 N 27 1 N7 A DG 11 ? ? C8 A DG 11 ? ? N9 A DG 11 ? ? 117.63 113.10 4.53 0.50 N 28 1 C8 A DG 11 ? ? N9 A DG 11 ? ? C4 A DG 11 ? ? 103.60 106.40 -2.80 0.40 N 29 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 112.88 108.30 4.58 0.30 N 30 1 "O3'" B DC 12 ? ? P B DT 13 ? ? "O5'" B DT 13 ? ? 65.92 104.00 -38.08 1.90 Y 31 1 "O3'" B DC 12 ? ? P B DT 13 ? ? OP2 B DT 13 ? ? 72.11 105.20 -33.09 2.20 Y 32 1 "O3'" B DC 12 ? ? P B DT 13 ? ? OP1 B DT 13 ? ? 121.43 110.50 10.93 1.10 Y 33 1 OP1 B DT 13 ? ? P B DT 13 ? ? OP2 B DT 13 ? ? 105.95 119.60 -13.65 1.50 N 34 1 "O5'" B DT 13 ? ? P B DT 13 ? ? OP1 B DT 13 ? ? 90.22 105.70 -15.48 0.90 N 35 1 "O5'" B DT 13 ? ? P B DT 13 ? ? OP2 B DT 13 ? ? 137.40 110.70 26.70 1.20 N 36 1 "O4'" B DT 13 ? ? "C1'" B DT 13 ? ? N1 B DT 13 ? ? 110.73 108.30 2.43 0.30 N 37 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 111.29 108.30 2.99 0.30 N 38 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 110.86 108.30 2.56 0.30 N 39 1 "O4'" B DT 16 ? ? "C1'" B DT 16 ? ? N1 B DT 16 ? ? 111.42 108.30 3.12 0.30 N 40 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 111.23 108.30 2.93 0.30 N 41 1 "O4'" B DG 18 ? ? "C1'" B DG 18 ? ? N9 B DG 18 ? ? 110.91 108.30 2.61 0.30 N 42 1 N7 B DG 18 ? ? C8 B DG 18 ? ? N9 B DG 18 ? ? 117.52 113.10 4.42 0.50 N 43 1 C8 B DG 18 ? ? N9 B DG 18 ? ? C4 B DG 18 ? ? 103.89 106.40 -2.51 0.40 N 44 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 110.97 108.30 2.67 0.30 N 45 1 "O4'" B DC 20 ? ? "C1'" B DC 20 ? ? N1 B DC 20 ? ? 110.47 108.30 2.17 0.30 N 46 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 111.02 108.30 2.72 0.30 N 47 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 110.46 108.30 2.16 0.30 N 48 1 N7 B DG 22 ? ? C8 B DG 22 ? ? N9 B DG 22 ? ? 117.56 113.10 4.46 0.50 N 49 1 C8 B DG 22 ? ? N9 B DG 22 ? ? C4 B DG 22 ? ? 103.72 106.40 -2.68 0.40 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1AGO 'double helix' 1AGO 'b-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 11 1_555 0.745 -0.435 0.113 -7.394 -5.949 0.202 1 A_DC1:DG22_B A 1 ? B 22 ? 19 1 1 A DG 2 1_555 B DC 10 1_555 -0.704 -0.368 0.149 4.472 -10.680 -0.778 2 A_DG2:DC21_B A 2 ? B 21 ? 19 1 1 A DG 3 1_555 B DC 9 1_555 -0.330 -0.163 0.025 4.337 -15.417 -1.809 3 A_DG3:DC20_B A 3 ? B 20 ? 19 1 1 A DA 4 1_555 B DT 8 1_555 0.486 -0.170 -0.212 3.123 -19.658 -3.245 4 A_DA4:DT19_B A 4 ? B 19 ? 20 1 1 A DC 5 1_555 B DG 7 1_555 0.254 -0.128 -0.150 2.506 -17.503 2.120 5 A_DC5:DG18_B A 5 ? B 18 ? 19 1 1 A DA 6 1_555 B DT 6 1_555 0.222 -0.201 -0.218 -9.662 -9.156 -8.117 6 A_DA6:DT17_B A 6 ? B 17 ? 20 1 1 A Y 7 1_555 B DT 5 1_555 0.246 -0.036 0.218 6.689 -14.084 -3.744 7 A_Y7:DT16_B A 7 ? B 16 ? 20 1 1 A DG 8 1_555 B DC 4 1_555 -0.527 -0.201 0.040 7.240 -10.254 1.424 8 A_DG8:DC15_B A 8 ? B 15 ? 19 1 1 A DA 9 1_555 B DT 3 1_555 0.412 -0.141 -0.047 17.952 -14.993 -1.289 9 A_DA9:DT14_B A 9 ? B 14 ? 20 1 1 A DA 10 1_555 B DT 2 1_555 0.299 -0.122 0.052 22.738 -15.616 5.088 10 A_DA10:DT13_B A 10 ? B 13 ? 20 1 1 A DG 11 1_555 B DC 1 1_555 -1.038 -0.293 0.562 27.541 0.046 0.054 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 DC 1 1_555 B DG 11 1_555 A DG 2 1_555 B DC 10 1_555 -0.221 0.723 2.891 -0.522 5.545 32.387 0.421 0.311 2.973 9.850 0.927 32.850 1 AA_DC1DG2:DC21DG22_BB A 1 ? B 22 ? A 2 ? B 21 ? 1 A DG 2 1_555 B DC 10 1_555 A DG 3 1_555 B DC 9 1_555 0.442 0.213 3.405 3.170 -4.271 37.290 0.908 -0.256 3.385 -6.638 -4.926 37.654 2 AA_DG2DG3:DC20DC21_BB A 2 ? B 21 ? A 3 ? B 20 ? 1 A DG 3 1_555 B DC 9 1_555 A DA 4 1_555 B DT 8 1_555 0.400 0.195 3.328 2.454 1.085 39.043 0.158 -0.296 3.350 1.621 -3.666 39.132 3 AA_DG3DA4:DT19DC20_BB A 3 ? B 20 ? A 4 ? B 19 ? 1 A DA 4 1_555 B DT 8 1_555 A DC 5 1_555 B DG 7 1_555 0.291 -0.160 3.081 1.848 -1.522 36.443 -0.057 -0.223 3.095 -2.430 -2.952 36.519 4 AA_DA4DC5:DG18DT19_BB A 4 ? B 19 ? A 5 ? B 18 ? 1 A DC 5 1_555 B DG 7 1_555 A DA 6 1_555 B DT 6 1_555 -1.006 0.108 3.688 -5.281 4.967 39.456 -0.494 0.775 3.773 7.283 7.742 40.090 5 AA_DC5DA6:DT17DG18_BB A 5 ? B 18 ? A 6 ? B 17 ? 1 A DA 6 1_555 B DT 6 1_555 A Y 7 1_555 B DT 5 1_555 0.617 -0.228 2.829 1.238 -8.057 34.728 0.653 -0.851 2.829 -13.273 -2.039 35.643 6 AA_DA6Y7:DT16DT17_BB A 6 ? B 17 ? A 7 ? B 16 ? 1 A Y 7 1_555 B DT 5 1_555 A DG 8 1_555 B DC 4 1_555 0.464 -0.467 3.097 0.648 1.460 31.035 -1.137 -0.749 3.082 2.727 -1.209 31.075 7 AA_Y7DG8:DC15DT16_BB A 7 ? B 16 ? A 8 ? B 15 ? 1 A DG 8 1_555 B DC 4 1_555 A DA 9 1_555 B DT 3 1_555 0.131 0.371 3.005 3.549 -1.316 41.924 0.641 0.155 2.993 -1.834 -4.947 42.087 8 AA_DG8DA9:DT14DC15_BB A 8 ? B 15 ? A 9 ? B 14 ? 1 A DA 9 1_555 B DT 3 1_555 A DA 10 1_555 B DT 2 1_555 0.704 0.321 3.263 1.301 -0.741 36.477 0.614 -0.943 3.278 -1.184 -2.078 36.506 9 AA_DA9DA10:DT13DT14_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 -0.413 -0.169 2.950 -5.597 4.314 32.713 -0.942 -0.124 2.933 7.550 9.795 33.447 10 AA_DA10DG11:DC12DT13_BB A 10 ? B 13 ? A 11 ? B 12 ? #