data_219D # _entry.id 219D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _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 219D pdb_0000219d 10.2210/pdb219d/pdb WWPDB D_1000177585 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 219D _pdbx_database_status.recvd_initial_deposition_date 1995-07-25 _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 'Gonzalez, C.' 1 'James, T.L.' 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 ;Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints. ; Biochemistry 34 4969 4982 1995 BICHAW US 0006-2960 0033 ? 7711019 10.1021/bi00015a008 1 ;Structural Study of a DNA(Dot)RNA Hybrid Duplex with a Chiral Phosphorothioate Moiety by NMR: Extraction of Distance and Torsion Angle Constraints and Imino Proton Exchange Rates ; Biochemistry 33 11062 ? 1994 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Gonzalez, C.' 1 ? primary 'Stec, W.' 2 ? primary 'Reynolds, M.A.' 3 ? primary 'James, T.L.' 4 ? 1 'Gonzalez, C.' 5 ? 1 'Stec, W.' 6 ? 1 'Kobylanska, A.' 7 ? 1 'Hogrefe, R.I.' 8 ? 1 'Reynolds, M.A.' 9 ? 1 'James, T.L.' 10 ? # _cell.entry_id 219D _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 219D _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(*GP*CP*TP*AP*TP*AP*AP*TP*GP*G)-3') ; 3100.106 1 ? ? ? 'PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8' 2 polymer syn ;RNA (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') ; 3121.908 1 ? ? ? 'PHOSPHOROTHIOATE LINK BETWEEN A 7 AND T 8' # loop_ _entity_keywords.entity_id _entity_keywords.text 1 'DEOXYRIBONUCLEIC ACID' 2 'RIBONUCLEIC ACID' # 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 '(DG)(DC)(DT)(DA)(DT)(DA)(DA)(PST)(DG)(DG)' GCTATAATGG A ? 2 polyribonucleotide no no CCAUUAUAGC CCAUUAUAGC B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DC n 1 3 DT n 1 4 DA n 1 5 DT n 1 6 DA n 1 7 DA n 1 8 PST n 1 9 DG n 1 10 DG n 2 1 C n 2 2 C n 2 3 A n 2 4 U n 2 5 U n 2 6 A n 2 7 U n 2 8 A n 2 9 G n 2 10 C n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _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 1 1 sample ? ? ? ? ? 'CHEMICALLY SYNTHESIZED' 2 1 sample ? ? ? ? ? 'CHEMICALLY SYNTHESIZED' # 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 219D 219D ? ? ? 2 2 PDB 219D 219D ? ? ? # 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 219D A 1 ? 10 ? 219D 1 ? 10 ? 1 10 2 2 219D B 1 ? 10 ? 219D 11 ? 20 ? 11 20 # 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 A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 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 PST 'DNA linking' n "THYMIDINE-5'-THIOPHOSPHATE" ? 'C10 H15 N2 O7 P S' 338.274 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _pdbx_nmr_refine.entry_id 219D _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ;NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 411 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 219D _pdbx_nmr_details.text ;THE PHOSPHATE BETWEEN NUCLEOTIDES SEVEN AND EIGHT IS MODIFIED BY SUBSTITUTING A SULFUR FOR ONE OF THE OXYGEN ATOMS. TWO SAMPLES WITH PURE CHIRALITY (R OR S) HAVE BEEN STUDIED; ONLY MINOR DIFFERENCES COULD BE DETECTED. THE COORDINATES REPRESENT THE S STEREOISOMER OF THE MODIFIED PHOSPHATE. THE SIXTH ROOT R-FACTOR, EXPRESSING THE FIT TO THE EXPERIMENTAL NOE DATA, CALCULATED WITH THE PROGRAM CORMA (KEEPERS AND JAMES), HAS A VALUE OF 0.074. THE ROOT MEAN SQUARE DEVIATION BETWEEN EXPERIMENTAL AND THEORETICAL DEOXYRIBOSE J-COUPLING CONSTRAINTS IS 2.01 HZ. THIS POOR FIT OF THE COUPLING CONSTANTS IS DUE TO CONFORMATIONAL FLEXIBILITY IN THE SUGAR RING. ; # _pdbx_nmr_ensemble.entry_id 219D _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 AMBER4 _pdbx_nmr_software.version ? _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors PEARLMAN,KOLLMAN _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 219D _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 219D _struct.title ;DNA/RNA HYBRID DUPLEX (5'-D(*GP*CP*TP*AP*TP*AP*APS*TP*GP*G)-3')(DOT) (5'-R(*CP*CP*AP*UP*UP*AP*UP*AP*GP*C)-3') WITH A PHOSPHOROTHIOATE MOIETY ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 219D _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'DNA, RNA, HYBRID, PHOSPHOROTHIOATE, 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 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 7 "O3'" ? ? ? 1_555 A PST 8 P ? ? A DA 7 A PST 8 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale2 covale both ? A PST 8 "O3'" ? ? ? 1_555 A DG 9 P ? ? A PST 8 A DG 9 1_555 ? ? ? ? ? ? ? 1.613 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B C 10 N3 ? ? A DG 1 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B C 10 O2 ? ? A DG 1 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B C 10 N4 ? ? A DG 1 B C 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B G 9 N1 ? ? A DC 2 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B G 9 O6 ? ? A DC 2 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B G 9 N2 ? ? A DC 2 B G 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B A 8 N1 ? ? A DT 3 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B A 8 N6 ? ? A DT 3 B A 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B U 7 N3 ? ? A DA 4 B U 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B U 7 O4 ? ? A DA 4 B U 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B A 6 N1 ? ? A DT 5 B A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B A 6 N6 ? ? A DT 5 B A 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B U 5 N3 ? ? A DA 6 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B U 5 O4 ? ? A DA 6 B U 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B U 4 N3 ? ? A DA 7 B U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B U 4 O4 ? ? A DA 7 B U 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A PST 8 N3 ? ? ? 1_555 B A 3 N1 ? ? A PST 8 B A 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A PST 8 O4 ? ? ? 1_555 B A 3 N6 ? ? A PST 8 B A 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B C 2 N3 ? ? A DG 9 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B C 2 O2 ? ? A DG 9 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B C 2 N4 ? ? A DG 9 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B C 1 N3 ? ? A DG 10 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B C 1 O2 ? ? A DG 10 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B C 1 N4 ? ? A DG 10 B C 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 219D _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 219D _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 N O P S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG G A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A 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 DA 7 7 7 DA A A . n A 1 8 PST 8 8 8 PST T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n B 2 1 C 1 11 11 C C B . n B 2 2 C 2 12 12 C C B . n B 2 3 A 3 13 13 A A B . n B 2 4 U 4 14 14 U U B . n B 2 5 U 5 15 15 U U B . n B 2 6 A 6 16 16 A A B . n B 2 7 U 7 17 17 U U B . n B 2 8 A 8 18 18 A A B . n B 2 9 G 9 19 19 G G B . n B 2 10 C 10 20 20 C C B . n # _pdbx_struct_mod_residue.id 1 _pdbx_struct_mod_residue.label_asym_id A _pdbx_struct_mod_residue.label_comp_id PST _pdbx_struct_mod_residue.label_seq_id 8 _pdbx_struct_mod_residue.auth_asym_id A _pdbx_struct_mod_residue.auth_comp_id PST _pdbx_struct_mod_residue.auth_seq_id 8 _pdbx_struct_mod_residue.PDB_ins_code ? _pdbx_struct_mod_residue.parent_comp_id DT _pdbx_struct_mod_residue.details "THYMIDINE-5'-THIOPHOSPHATE" # _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 1995-10-15 2 'Structure model' 1 1 2008-03-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-09 # _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' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 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_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 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' '_pdbx_database_status.process_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _software.name AMBER _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "C4'" A DG 1 ? ? "C3'" A DG 1 ? ? "C2'" A DG 1 ? ? 96.85 102.20 -5.35 0.70 N 2 1 "O4'" A DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 113.00 108.30 4.70 0.30 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? "C2'" A DC 2 ? ? 109.99 106.80 3.19 0.50 N 4 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? N1 A DC 2 ? ? 112.17 108.30 3.87 0.30 N 5 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? "C2'" A DT 3 ? ? 100.96 105.90 -4.94 0.80 N 6 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.65 122.90 -4.25 0.60 N 7 1 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? "C1'" A DA 4 ? ? 110.86 102.50 8.36 1.20 N 8 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 111.25 108.30 2.95 0.30 N 9 1 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 118.48 122.90 -4.42 0.60 N 10 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 110.46 108.30 2.16 0.30 N 11 1 "O4'" A DA 7 ? ? "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? 110.70 106.00 4.70 0.60 N 12 1 "C4'" A DA 7 ? ? "C3'" A DA 7 ? ? "C2'" A DA 7 ? ? 92.50 102.20 -9.70 0.70 N 13 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? "C2'" A DA 7 ? ? 95.67 105.90 -10.23 0.80 N 14 1 "O4'" A DA 7 ? ? "C1'" A DA 7 ? ? N9 A DA 7 ? ? 116.46 108.30 8.16 0.30 N 15 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 111.01 108.30 2.71 0.30 N 16 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 110.50 108.30 2.20 0.30 N 17 1 "O4'" B C 12 ? ? "C1'" B C 12 ? ? N1 B C 12 ? ? 113.21 108.50 4.71 0.70 N 18 1 "O4'" B A 13 ? ? "C1'" B A 13 ? ? N9 B A 13 ? ? 113.77 108.50 5.27 0.70 N 19 1 "O4'" B U 14 ? ? "C1'" B U 14 ? ? N1 B U 14 ? ? 114.86 108.50 6.36 0.70 N 20 1 "O4'" B U 15 ? ? "C1'" B U 15 ? ? N1 B U 15 ? ? 112.83 108.50 4.33 0.70 N 21 1 "C3'" B A 16 ? ? "C2'" B A 16 ? ? "C1'" B A 16 ? ? 106.33 101.50 4.83 0.80 N 22 1 "O4'" B A 16 ? ? "C1'" B A 16 ? ? N9 B A 16 ? ? 114.37 108.50 5.87 0.70 N 23 1 "O4'" B U 17 ? ? "C1'" B U 17 ? ? N1 B U 17 ? ? 113.25 108.50 4.75 0.70 N 24 1 "C5'" B A 18 ? ? "C4'" B A 18 ? ? "O4'" B A 18 ? ? 115.49 109.80 5.69 0.90 N 25 1 "C3'" B A 18 ? ? "C2'" B A 18 ? ? "C1'" B A 18 ? ? 107.57 101.50 6.07 0.80 N 26 1 "O4'" B C 20 ? ? "C1'" B C 20 ? ? N1 B C 20 ? ? 114.26 108.50 5.76 0.70 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 DG A 1 ? ? 0.066 'SIDE CHAIN' 2 1 DA A 6 ? ? 0.067 'SIDE CHAIN' 3 1 DA A 7 ? ? 0.070 'SIDE CHAIN' 4 1 C B 11 ? ? 0.091 'SIDE CHAIN' 5 1 C B 12 ? ? 0.067 'SIDE CHAIN' 6 1 A B 13 ? ? 0.109 'SIDE CHAIN' 7 1 A B 18 ? ? 0.073 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 219D 'double helix' 219D 'a-form double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 B C 10 1_555 -0.001 -0.118 0.068 -3.689 -15.806 -1.221 1 A_DG1:C20_B A 1 ? B 20 ? 19 1 1 A DC 2 1_555 B G 9 1_555 0.349 -0.169 0.212 -4.601 -7.025 -2.376 2 A_DC2:G19_B A 2 ? B 19 ? 19 1 1 A DT 3 1_555 B A 8 1_555 -0.399 -0.044 0.286 3.262 -4.037 -2.052 3 A_DT3:A18_B A 3 ? B 18 ? 20 1 1 A DA 4 1_555 B U 7 1_555 0.185 -0.158 0.399 9.530 -11.483 -2.865 4 A_DA4:U17_B A 4 ? B 17 ? 20 1 1 A DT 5 1_555 B A 6 1_555 -0.327 -0.089 -0.039 11.807 -21.481 -3.505 5 A_DT5:A16_B A 5 ? B 16 ? 20 1 1 A DA 6 1_555 B U 5 1_555 0.209 -0.117 -0.552 4.214 -16.615 -5.491 6 A_DA6:U15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B U 4 1_555 0.303 -0.085 0.027 0.726 -25.069 -6.868 7 A_DA7:U14_B A 7 ? B 14 ? 20 1 1 A PST 8 1_555 B A 3 1_555 -0.218 -0.035 -0.128 11.397 -21.863 -6.744 8 A_PST8:A13_B A 8 ? B 13 ? 20 1 1 A DG 9 1_555 B C 2 1_555 -0.099 -0.154 0.388 -2.083 -18.964 -4.127 9 A_DG9:C12_B A 9 ? B 12 ? 19 1 1 A DG 10 1_555 B C 1 1_555 -0.317 -0.251 0.205 -10.690 -30.466 -3.993 10 A_DG10:C11_B A 10 ? B 11 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 B C 10 1_555 A DC 2 1_555 B G 9 1_555 -0.564 -1.525 3.123 -2.734 5.826 37.079 -3.066 0.546 2.892 9.077 4.260 37.614 1 AA_DG1DC2:G19C20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A DC 2 1_555 B G 9 1_555 A DT 3 1_555 B A 8 1_555 -0.451 -1.438 2.876 -2.438 0.919 24.945 -3.549 0.405 2.852 2.119 5.625 25.079 2 AA_DC2DT3:A18G19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A DT 3 1_555 B A 8 1_555 A DA 4 1_555 B U 7 1_555 -0.024 -1.565 2.719 -1.537 7.879 37.829 -3.126 -0.112 2.357 11.987 2.339 38.641 3 AA_DT3DA4:U17A18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DA 4 1_555 B U 7 1_555 A DT 5 1_555 B A 6 1_555 0.201 -1.332 3.168 2.590 -0.159 34.296 -2.228 0.053 3.180 -0.269 -4.384 34.391 4 AA_DA4DT5:A16U17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DT 5 1_555 B A 6 1_555 A DA 6 1_555 B U 5 1_555 -0.136 -1.155 3.491 8.572 25.310 31.846 -4.243 1.076 1.996 38.725 -13.115 41.348 5 AA_DT5DA6:U15A16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DA 6 1_555 B U 5 1_555 A DA 7 1_555 B U 4 1_555 0.085 -0.880 3.076 -6.461 6.848 33.899 -2.392 -1.023 2.788 11.473 10.824 35.145 6 AA_DA6DA7:U14U15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B U 4 1_555 A PST 8 1_555 B A 3 1_555 -0.549 -0.202 2.897 1.007 -1.669 35.014 -0.114 1.044 2.887 -2.772 -1.671 35.066 7 AA_DA7PST8:A13U14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A PST 8 1_555 B A 3 1_555 A DG 9 1_555 B C 2 1_555 0.092 -1.223 3.360 -3.007 12.624 33.130 -3.782 -0.575 2.711 21.156 5.039 35.515 8 AA_PST8DG9:C12A13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B C 2 1_555 A DG 10 1_555 B C 1 1_555 0.109 -1.029 3.404 1.788 6.867 31.272 -3.112 0.128 3.114 12.537 -3.265 32.048 9 AA_DG9DG10:C11C12_BB A 9 ? B 12 ? A 10 ? B 11 ? #