data_1DHH # _entry.id 1DHH # _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 1DHH pdb_00001dhh 10.2210/pdb1dhh/pdb WWPDB D_1000172781 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1DRN _pdbx_database_related.details 'MINIMIZED AVERAGE STRUCTURE' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DHH _pdbx_database_status.recvd_initial_deposition_date 1995-10-18 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _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 'Nishizaki, T.' 1 'Iwai, S.' 2 'Ohkubo, T.' 3 'Kojima, C.' 4 'Nakamura, H.' 5 'Kyogoku, Y.' 6 'Ohtsuka, E.' 7 # _citation.id primary _citation.title ;Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC). ; _citation.journal_abbrev Biochemistry _citation.journal_volume 35 _citation.page_first 4016 _citation.page_last 4025 _citation.year 1996 _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 8672435 _citation.pdbx_database_id_DOI 10.1021/bi9519821 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nishizaki, T.' 1 ? primary 'Iwai, S.' 2 ? primary 'Ohkubo, T.' 3 ? primary 'Kojima, C.' 4 ? primary 'Nakamura, H.' 5 ? primary 'Kyogoku, Y.' 6 ? primary 'Ohtsuka, E.' 7 ? # _cell.entry_id 1DHH _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 1DHH _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/RNA (5'-D(*GP*G)-R(P*AP*GP*AP*U)-D(P*GP*AP*C)-3') ; 2854.832 1 ? ? ? 'CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA' 2 polymer syn ;DNA (5'-D(*GP*TP*CP*AP*TP*CP*TP*CP*C)-3') ; 2666.761 1 ? ? ? 'CRYSTALLIZATION CONDITIONS\: PH 7.0, 298K, 100MM NACL, 50MM NA PHOSPHATE, 3MM EDTA' # loop_ _entity_keywords.entity_id _entity_keywords.text 1 'RIBONUCLEIC ACID' 2 'DEOXYRIBONUCLEIC ACID/RIBONUCLEIC ACID' # loop_ _entity_name_com.entity_id _entity_name_com.name 1 DHD 2 DHD # 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/polyribonucleotide hybrid' no no '(DG)(DG)AGAU(DG)(DA)(DC)' GGAGAUGAC A ? 2 polydeoxyribonucleotide no no '(DG)(DT)(DC)(DA)(DT)(DC)(DT)(DC)(DC)' GTCATCTCC 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 DG n 1 3 A n 1 4 G n 1 5 A n 1 6 U n 1 7 DG n 1 8 DA n 1 9 DC n 2 1 DG n 2 2 DT n 2 3 DC n 2 4 DA n 2 5 DT n 2 6 DC n 2 7 DT n 2 8 DC n 2 9 DC 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 ? ? ? ? ? 'A SUBSTRATE OF RNASE H' 2 1 sample ? ? ? ? ? 'A SUBSTRATE OF RNASE H' # 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 1DHH 1DHH ? ? ? 2 2 PDB 1DHH 1DHH ? ? ? # 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 1DHH A 1 ? 9 ? 1DHH 1 ? 9 ? 1 9 2 2 1DHH B 1 ? 9 ? 1DHH 10 ? 18 ? 10 18 # 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 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 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_refine.entry_id 1DHH _pdbx_nmr_refine.method 'MOLECULAR DYNAMICS, MATRIX RELAXATION' _pdbx_nmr_refine.details ;RMSD BOND DISTANCES 0.0077 ANGSTROMS RMSD BOND ANGLES 1.40 DEGREES NUMBER OF ATOMS USED IN REFINEMENT. NUMBER OF PROTEIN ATOMS 0 NUMBER OF NUCLEIC ACID ATOMS 366 NUMBER OF HETEROGEN ATOMS 0 NUMBER OF SOLVENT ATOMS 0 THE STRUCTURES WAS REFINED BY A COMBINATION OF RESTRAINED MOLECULAR DYNAMICS USING THE X-PLOR (V3.1F) PROGRAM (BRUNGER 1988) AND FULL RELAXATION MATRIX REFINEMENT OF THE TWO-DIMENSIONAL NUCLEAR OVERHAUSER EFFECT SPECTRUM AT 150 MSEC. ; _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 1DHH _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 X-PLOR _pdbx_nmr_software.version 3.1F _pdbx_nmr_software.classification refinement _pdbx_nmr_software.authors BRUNGER _pdbx_nmr_software.ordinal 1 # _exptl.entry_id 1DHH _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1DHH _struct.title 'NMR SOLUTION STRUCTURE OF THE DNA DUPLEX CONTAINING DNA/RNA HYBRID REGION, D(GG)R(AGAU)D(GAC)/D(GTCATCTCC)' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DHH _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'DNA/RNA HYBRID IN DNA DUPLEX, 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 _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 _struct_conn.pdbx_role hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 1 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 1 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 1 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 8 N3 ? ? A DG 2 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 8 O2 ? ? A DG 2 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 8 N4 ? ? A DG 2 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A A 3 N1 ? ? ? 1_555 B DT 7 N3 ? ? A A 3 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A A 3 N6 ? ? ? 1_555 B DT 7 O4 ? ? A A 3 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 4 N1 ? ? ? 1_555 B DC 6 N3 ? ? A G 4 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A G 4 N2 ? ? ? 1_555 B DC 6 O2 ? ? A G 4 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A G 4 O6 ? ? ? 1_555 B DC 6 N4 ? ? A G 4 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A A 5 N1 ? ? ? 1_555 B DT 5 N3 ? ? A A 5 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A A 5 N6 ? ? ? 1_555 B DT 5 O4 ? ? A A 5 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A U 6 N3 ? ? ? 1_555 B DA 4 N1 ? ? A U 6 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A U 6 O4 ? ? ? 1_555 B DA 4 N6 ? ? A U 6 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 7 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 7 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 7 B DC 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 2 N3 ? ? A DA 8 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 2 O4 ? ? A DA 8 B DT 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 9 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 9 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 9 B DG 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1DHH _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 1DHH _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 # 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 DG 2 2 2 DG G A . n A 1 3 A 3 3 3 A A A . n A 1 4 G 4 4 4 G G A . n A 1 5 A 5 5 5 A A A . n A 1 6 U 6 6 6 U U A . n A 1 7 DG 7 7 7 DG G A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 DC 9 9 9 DC C A . n B 2 1 DG 1 10 10 DG G B . n B 2 2 DT 2 11 11 DT T B . n B 2 3 DC 3 12 12 DC C B . n B 2 4 DA 4 13 13 DA A B . n B 2 5 DT 5 14 14 DT T B . n B 2 6 DC 6 15 15 DC C B . n B 2 7 DT 7 16 16 DT T B . n B 2 8 DC 8 17 17 DC C B . n B 2 9 DC 9 18 18 DC C 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 1996-04-03 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' '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 # 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' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement . ? 2 X-PLOR phasing . ? 3 # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 NACL 100 mM ? 1 'NA PHOSPHATE' 50 mM ? 1 EDTA 3 mM ? # 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 DG 1 ? ? "C1'" A DG 1 ? ? N9 A DG 1 ? ? 112.36 108.30 4.06 0.30 N 2 1 N7 A DG 1 ? ? C8 A DG 1 ? ? N9 A DG 1 ? ? 117.49 113.10 4.39 0.50 N 3 1 C8 A DG 1 ? ? N9 A DG 1 ? ? C4 A DG 1 ? ? 103.71 106.40 -2.69 0.40 N 4 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.52 108.30 4.22 0.30 N 5 1 N7 A DG 2 ? ? C8 A DG 2 ? ? N9 A DG 2 ? ? 117.72 113.10 4.62 0.50 N 6 1 C8 A DG 2 ? ? N9 A DG 2 ? ? C4 A DG 2 ? ? 103.95 106.40 -2.45 0.40 N 7 1 N7 A A 3 ? ? C8 A A 3 ? ? N9 A A 3 ? ? 117.64 113.80 3.84 0.50 N 8 1 "C3'" A G 4 ? ? "C2'" A G 4 ? ? "C1'" A G 4 ? ? 106.93 101.50 5.43 0.80 N 9 1 N7 A G 4 ? ? C8 A G 4 ? ? N9 A G 4 ? ? 117.66 113.10 4.56 0.50 N 10 1 "C3'" A A 5 ? ? "C2'" A A 5 ? ? "C1'" A A 5 ? ? 106.48 101.50 4.98 0.80 N 11 1 N7 A A 5 ? ? C8 A A 5 ? ? N9 A A 5 ? ? 118.05 113.80 4.25 0.50 N 12 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.87 108.30 2.57 0.30 N 13 1 N7 A DG 7 ? ? C8 A DG 7 ? ? N9 A DG 7 ? ? 117.86 113.10 4.76 0.50 N 14 1 C8 A DG 7 ? ? N9 A DG 7 ? ? C4 A DG 7 ? ? 103.97 106.40 -2.43 0.40 N 15 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 110.84 108.30 2.54 0.30 N 16 1 N7 A DA 8 ? ? C8 A DA 8 ? ? N9 A DA 8 ? ? 117.61 113.80 3.81 0.50 N 17 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 111.36 108.30 3.06 0.30 N 18 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? N9 B DG 10 ? ? 111.25 108.30 2.95 0.30 N 19 1 N7 B DG 10 ? ? C8 B DG 10 ? ? N9 B DG 10 ? ? 117.73 113.10 4.63 0.50 N 20 1 C8 B DG 10 ? ? N9 B DG 10 ? ? C4 B DG 10 ? ? 103.82 106.40 -2.58 0.40 N 21 1 "O4'" B DT 11 ? ? "C1'" B DT 11 ? ? N1 B DT 11 ? ? 111.63 108.30 3.33 0.30 N 22 1 "O4'" B DC 12 ? ? "C1'" B DC 12 ? ? N1 B DC 12 ? ? 110.82 108.30 2.52 0.30 N 23 1 "O4'" B DA 13 ? ? "C1'" B DA 13 ? ? N9 B DA 13 ? ? 110.60 108.30 2.30 0.30 N 24 1 N7 B DA 13 ? ? C8 B DA 13 ? ? N9 B DA 13 ? ? 117.56 113.80 3.76 0.50 N 25 1 "O4'" B DT 14 ? ? "C1'" B DT 14 ? ? N1 B DT 14 ? ? 110.66 108.30 2.36 0.30 N 26 1 "O4'" B DC 15 ? ? "C1'" B DC 15 ? ? N1 B DC 15 ? ? 111.09 108.30 2.79 0.30 N 27 1 "O4'" B DT 16 ? ? "C1'" B DT 16 ? ? N1 B DT 16 ? ? 110.89 108.30 2.59 0.30 N 28 1 "O4'" B DC 17 ? ? "C1'" B DC 17 ? ? N1 B DC 17 ? ? 110.95 108.30 2.65 0.30 N 29 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 112.59 108.30 4.29 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 A A 3 ? ? 0.052 'SIDE CHAIN' 2 1 U A 6 ? ? 0.057 'SIDE CHAIN' # _ndb_struct_conf_na.entry_id 1DHH _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 DG 1 1_555 B DC 9 1_555 -0.530 -0.306 -0.185 -2.266 0.102 1.153 1 A_DG1:DC18_B A 1 ? B 18 ? 19 1 1 A DG 2 1_555 B DC 8 1_555 -0.694 -0.321 -0.076 -3.103 -4.593 5.848 2 A_DG2:DC17_B A 2 ? B 17 ? 19 1 1 A A 3 1_555 B DT 7 1_555 -0.342 -0.370 0.180 2.053 -8.970 4.670 3 A_A3:DT16_B A 3 ? B 16 ? 20 1 1 A G 4 1_555 B DC 6 1_555 -0.225 -0.303 0.086 4.345 -10.176 1.710 4 A_G4:DC15_B A 4 ? B 15 ? 19 1 1 A A 5 1_555 B DT 5 1_555 -0.412 -0.242 0.115 -3.696 -4.093 -5.726 5 A_A5:DT14_B A 5 ? B 14 ? 20 1 1 A U 6 1_555 B DA 4 1_555 0.165 -0.201 -0.193 8.703 -7.978 10.088 6 A_U6:DA13_B A 6 ? B 13 ? 20 1 1 A DG 7 1_555 B DC 3 1_555 0.161 -0.310 -0.290 -7.184 -1.884 0.778 7 A_DG7:DC12_B A 7 ? B 12 ? 19 1 1 A DA 8 1_555 B DT 2 1_555 -0.433 -0.380 0.018 0.601 -1.969 -0.505 8 A_DA8:DT11_B A 8 ? B 11 ? 20 1 1 A DC 9 1_555 B DG 1 1_555 0.615 -0.430 -0.044 2.282 -0.853 -1.240 9 A_DC9:DG10_B A 9 ? B 10 ? 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 DC 9 1_555 A DG 2 1_555 B DC 8 1_555 0.069 -1.396 3.332 -0.232 -0.339 28.939 -2.716 -0.190 3.347 -0.678 0.464 28.942 1 AA_DG1DG2:DC17DC18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A DG 2 1_555 B DC 8 1_555 A A 3 1_555 B DT 7 1_555 -0.855 0.146 3.609 -0.188 1.363 37.390 0.030 1.305 3.616 2.125 0.293 37.415 2 AA_DG2A3:DT16DC17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A A 3 1_555 B DT 7 1_555 A G 4 1_555 B DC 6 1_555 -0.562 0.707 3.424 1.801 16.843 33.415 -1.340 1.139 3.357 27.227 -2.911 37.354 3 AA_A3G4:DC15DT16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A G 4 1_555 B DC 6 1_555 A A 5 1_555 B DT 5 1_555 -1.226 -0.124 3.484 -5.761 15.473 28.785 -3.081 1.085 3.193 28.370 10.562 33.096 4 AA_G4A5:DT14DC15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A A 5 1_555 B DT 5 1_555 A U 6 1_555 B DA 4 1_555 1.136 -0.056 2.936 5.184 1.527 33.497 -0.322 -1.179 3.067 2.628 -8.923 33.918 5 AA_A5U6:DA13DT14_BB A 5 ? B 14 ? A 6 ? B 13 ? 1 A U 6 1_555 B DA 4 1_555 A DG 7 1_555 B DC 3 1_555 -0.446 0.949 3.827 0.601 35.887 38.689 -2.052 0.558 3.497 44.349 -0.743 52.301 6 AA_U6DG7:DC12DA13_BB A 6 ? B 13 ? A 7 ? B 12 ? 1 A DG 7 1_555 B DC 3 1_555 A DA 8 1_555 B DT 2 1_555 -0.319 -1.106 3.234 2.466 1.650 27.467 -2.708 1.252 3.123 3.463 -5.174 27.623 7 AA_DG7DA8:DT11DC12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DA 8 1_555 B DT 2 1_555 A DC 9 1_555 B DG 1 1_555 0.419 -1.099 3.272 -1.830 2.838 36.087 -2.159 -0.927 3.155 4.569 2.946 36.240 8 AA_DA8DC9:DG10DT11_BB A 8 ? B 11 ? A 9 ? B 10 ? #