data_104D # _entry.id 104D # _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 104D pdb_0000104d 10.2210/pdb104d/pdb WWPDB D_1000170010 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 104D _pdbx_database_status.recvd_initial_deposition_date 1994-12-16 _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 'Zhu, L.' 1 'Salazar, M.' 2 'Reid, B.R.' 3 # _citation.id primary _citation.title 'DNA duplexes flanked by hybrid duplexes: the solution structure of chimeric junctions in [r(cgcg)d(TATACGCG)]2.' _citation.journal_abbrev Biochemistry _citation.journal_volume 34 _citation.page_first 2372 _citation.page_last 2380 _citation.year 1995 _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 7857947 _citation.pdbx_database_id_DOI 10.1021/bi00007a033 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Zhu, L.' 1 ? primary 'Salazar, M.' 2 ? primary 'Reid, B.R.' 3 ? # _cell.entry_id 104D _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 104D _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA/RNA (5'-R(*CP*GP*CP*G)-D(P*TP*AP*TP*AP*CP*GP*CP*G)-3') ; _entity.formula_weight 3727.392 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_keywords.entity_id 1 _entity_keywords.text 'DEOXYRIBONUCLEIC ACID/RIBONUCLEIC ACID' # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'CGCG(DT)(DA)(DT)(DA)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGTATACGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 C n 1 2 G n 1 3 C n 1 4 G n 1 5 DT n 1 6 DA n 1 7 DT n 1 8 DA n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'CHEMICALLY SYNTHESIZED' # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 104D _struct_ref.pdbx_db_accession 104D _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 104D A 1 ? 12 ? 104D 1 ? 12 ? 1 12 2 1 104D B 1 ? 12 ? 104D 13 ? 24 ? 13 24 # 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 # _pdbx_nmr_refine.entry_id 104D _pdbx_nmr_refine.method ? _pdbx_nmr_refine.details ;R VALUE 0.160 FINAL RMS COORD. SHIFT 0.65 ANGSTROMS NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 766 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 104D _pdbx_nmr_ensemble.conformers_calculated_total_number ? _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria ? _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_software.name Discover _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors 'BIOSYM TECHNOLOGIES, INC.' _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 104D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 104D _struct.title 'DNA DUPLEXES FLANKED BY HYBRID DUPLEXES: THE SOLUTION STRUCTURE OF CHIMERIC JUNCTIONS IN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 104D _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'DNA, RNA, JUNCTION, HYBRID, DUPLEX, DNA-RNA COMPLEX, DNA-RNA HYBRID' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? # _struct_biol.id 1 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A C 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A C 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A C 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A C 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A C 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A C 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A G 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A G 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A G 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A G 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A G 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A G 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A C 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A C 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A C 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A C 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A C 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A C 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A G 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A G 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A G 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A G 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B DA 8 N1 ? ? A DT 5 B DA 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B DA 8 N6 ? ? A DT 5 B DA 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 5 N3 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 5 O4 ? ? A DA 8 B DT 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 4 N1 ? ? A DC 9 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 4 O6 ? ? A DC 9 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 4 N2 ? ? A DC 9 B G 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B C 3 N3 ? ? A DG 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B C 3 O2 ? ? A DG 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B C 3 N4 ? ? A DG 10 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B G 2 N1 ? ? A DC 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B G 2 O6 ? ? A DC 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B G 2 N2 ? ? A DC 11 B G 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B C 1 N3 ? ? A DG 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B C 1 O2 ? ? A DG 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B C 1 N4 ? ? A DG 12 B C 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 104D _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 104D _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 C 1 1 1 C C A . n A 1 2 G 2 2 2 G G A . n A 1 3 C 3 3 3 C C A . n A 1 4 G 4 4 4 G G A . n A 1 5 DT 5 5 5 DT T A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 C 1 13 13 C C B . n B 1 2 G 2 14 14 G G B . n B 1 3 C 3 15 15 C C B . n B 1 4 G 4 16 16 G G B . n B 1 5 DT 5 17 17 DT T B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DA 8 20 20 DA A B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 DG G 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 1995-03-31 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 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 # 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 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C8 _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 G _pdbx_validate_rmsd_bond.auth_seq_id_1 14 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 N9 _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 G _pdbx_validate_rmsd_bond.auth_seq_id_2 14 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.332 _pdbx_validate_rmsd_bond.bond_target_value 1.374 _pdbx_validate_rmsd_bond.bond_deviation -0.042 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.007 _pdbx_validate_rmsd_bond.linker_flag N # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C3'" A C 1 ? ? "C2'" A C 1 ? ? "C1'" A C 1 ? ? 106.82 101.50 5.32 0.80 N 2 1 "O4'" A C 1 ? ? "C1'" A C 1 ? ? N1 A C 1 ? ? 115.14 108.50 6.64 0.70 N 3 1 "C5'" A G 2 ? ? "C4'" A G 2 ? ? "O4'" A G 2 ? ? 115.81 109.80 6.01 0.90 N 4 1 "O4'" A G 2 ? ? "C1'" A G 2 ? ? N9 A G 2 ? ? 115.81 108.50 7.31 0.70 N 5 1 N7 A G 2 ? ? C8 A G 2 ? ? N9 A G 2 ? ? 116.96 113.10 3.86 0.50 N 6 1 "C5'" A C 3 ? ? "C4'" A C 3 ? ? "O4'" A C 3 ? ? 116.18 109.80 6.38 0.90 N 7 1 "O4'" A C 3 ? ? "C1'" A C 3 ? ? N1 A C 3 ? ? 114.12 108.50 5.62 0.70 N 8 1 "O4'" A G 4 ? ? "C1'" A G 4 ? ? N9 A G 4 ? ? 113.78 108.50 5.28 0.70 N 9 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 113.99 108.30 5.69 0.30 N 10 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 110.81 108.30 2.51 0.30 N 11 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 112.99 108.30 4.69 0.30 N 12 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 113.24 108.30 4.94 0.30 N 13 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 115.49 108.30 7.19 0.30 N 14 1 "O4'" A DG 12 ? ? "C1'" A DG 12 ? ? N9 A DG 12 ? ? 112.27 108.30 3.97 0.30 N 15 1 "C3'" B C 13 ? ? "C2'" B C 13 ? ? "C1'" B C 13 ? ? 106.59 101.50 5.09 0.80 N 16 1 "O4'" B C 13 ? ? "C1'" B C 13 ? ? N1 B C 13 ? ? 114.80 108.50 6.30 0.70 N 17 1 "C5'" B G 14 ? ? "C4'" B G 14 ? ? "O4'" B G 14 ? ? 115.99 109.80 6.19 0.90 N 18 1 "O4'" B G 14 ? ? "C1'" B G 14 ? ? N9 B G 14 ? ? 115.81 108.50 7.31 0.70 N 19 1 N7 B G 14 ? ? C8 B G 14 ? ? N9 B G 14 ? ? 116.98 113.10 3.88 0.50 N 20 1 "C5'" B C 15 ? ? "C4'" B C 15 ? ? "O4'" B C 15 ? ? 116.19 109.80 6.39 0.90 N 21 1 "O4'" B C 15 ? ? "C1'" B C 15 ? ? N1 B C 15 ? ? 114.43 108.50 5.93 0.70 N 22 1 "O4'" B G 16 ? ? "C1'" B G 16 ? ? N9 B G 16 ? ? 113.85 108.50 5.35 0.70 N 23 1 "O4'" B DT 17 ? ? "C1'" B DT 17 ? ? N1 B DT 17 ? ? 114.01 108.30 5.71 0.30 N 24 1 "O4'" B DA 18 ? ? "C1'" B DA 18 ? ? N9 B DA 18 ? ? 110.76 108.30 2.46 0.30 N 25 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 112.93 108.30 4.63 0.30 N 26 1 "O4'" B DC 21 ? ? "C1'" B DC 21 ? ? N1 B DC 21 ? ? 113.27 108.30 4.97 0.30 N 27 1 "O4'" B DG 22 ? ? "C1'" B DG 22 ? ? N9 B DG 22 ? ? 115.60 108.30 7.30 0.30 N 28 1 "O4'" B DG 24 ? ? "C1'" B DG 24 ? ? N9 B DG 24 ? ? 112.06 108.30 3.76 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 2 ? ? 0.068 'SIDE CHAIN' 2 1 DT A 5 ? ? 0.073 'SIDE CHAIN' 3 1 DA A 6 ? ? 0.129 'SIDE CHAIN' 4 1 DT A 7 ? ? 0.081 'SIDE CHAIN' 5 1 G B 14 ? ? 0.066 'SIDE CHAIN' 6 1 DT B 17 ? ? 0.076 'SIDE CHAIN' 7 1 DA B 18 ? ? 0.126 'SIDE CHAIN' 8 1 DT B 19 ? ? 0.081 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 104D _ndb_struct_conf_na.feature '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 C 1 1_555 B DG 12 1_555 1.137 -0.356 0.172 10.537 -24.591 0.239 1 A_C1:DG24_B A 1 ? B 24 ? 19 1 1 A G 2 1_555 B DC 11 1_555 -1.068 -0.350 0.296 3.528 -8.069 -2.060 2 A_G2:DC23_B A 2 ? B 23 ? 19 1 1 A C 3 1_555 B DG 10 1_555 0.086 -0.108 0.316 3.673 -15.486 -3.550 3 A_C3:DG22_B A 3 ? B 22 ? 19 1 1 A G 4 1_555 B DC 9 1_555 -0.560 -0.146 0.071 -11.989 -22.363 -0.281 4 A_G4:DC21_B A 4 ? B 21 ? 19 1 1 A DT 5 1_555 B DA 8 1_555 0.585 -0.155 0.272 -10.549 -13.895 3.168 5 A_DT5:DA20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 -0.513 -0.136 -0.110 -6.921 -22.807 -0.881 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 0.496 -0.129 -0.107 7.307 -22.819 -0.895 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DA 8 1_555 B DT 5 1_555 -0.593 -0.154 0.272 11.273 -13.873 3.218 8 A_DA8:DT17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B G 4 1_555 0.606 -0.160 0.050 12.697 -22.927 -0.073 9 A_DC9:G16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B C 3 1_555 -0.177 -0.117 0.295 -3.588 -15.118 -3.308 10 A_DG10:C15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B G 2 1_555 1.098 -0.355 0.265 -2.800 -8.001 -1.686 11 A_DC11:G14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B C 1 1_555 -1.135 -0.348 0.133 -12.291 -26.411 0.664 12 A_DG12:C13_B A 12 ? B 13 ? 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 C 1 1_555 B DG 12 1_555 A G 2 1_555 B DC 11 1_555 -0.364 -1.425 2.802 -2.424 16.995 29.601 -4.457 0.330 1.772 30.272 4.317 34.122 1 AA_C1G2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A G 2 1_555 B DC 11 1_555 A C 3 1_555 B DG 10 1_555 0.224 -1.321 3.061 -1.740 5.237 38.334 -2.576 -0.532 2.850 7.924 2.634 38.714 2 AA_G2C3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A C 3 1_555 B DG 10 1_555 A G 4 1_555 B DC 9 1_555 0.299 -2.073 3.101 3.564 17.778 27.619 -6.010 -0.055 1.545 33.103 -6.636 32.942 3 AA_C3G4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A G 4 1_555 B DC 9 1_555 A DT 5 1_555 B DA 8 1_555 0.308 -1.185 3.045 2.307 0.280 34.508 -2.033 -0.185 3.049 0.472 -3.884 34.584 4 AA_G4DT5:DA20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DT 5 1_555 B DA 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.221 -1.114 2.933 7.358 12.984 31.270 -3.535 1.313 2.207 22.550 -12.778 34.569 5 AA_DT5DA6:DT19DA20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.009 0.389 2.762 -0.103 -3.558 42.808 0.828 -0.021 2.723 -4.865 0.141 42.948 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DA 8 1_555 B DT 5 1_555 0.213 -1.139 2.921 -7.529 13.430 31.070 -3.616 -1.312 2.155 23.361 13.096 34.591 7 AA_DT7DA8:DT17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DA 8 1_555 B DT 5 1_555 A DC 9 1_555 B G 4 1_555 -0.311 -1.191 3.046 -2.252 0.437 34.583 -2.063 0.199 3.045 0.734 3.784 34.656 8 AA_DA8DC9:G16DT17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B G 4 1_555 A DG 10 1_555 B C 3 1_555 -0.318 -2.123 3.106 -3.768 18.656 26.807 -6.213 0.069 1.402 35.164 7.101 32.776 9 AA_DC9DG10:C15G16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B C 3 1_555 A DC 11 1_555 B G 2 1_555 -0.208 -1.306 3.050 1.793 5.329 38.571 -2.541 0.509 2.839 8.015 -2.697 38.963 10 AA_DG10DC11:G14C15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B G 2 1_555 A DG 12 1_555 B C 1 1_555 0.397 -1.457 2.845 2.816 18.318 29.860 -4.509 -0.338 1.722 31.970 -4.915 35.032 11 AA_DC11DG12:C13G14_BB A 11 ? B 14 ? A 12 ? B 13 ? #