data_7CLS # _entry.id 7CLS # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 7CLS pdb_00007cls 10.2210/pdb7cls/pdb WWPDB D_1300017687 ? ? BMRB 36364 ? ? # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'Solution structure of an intramolecular G-quadruplex containing a duplex bulge' _pdbx_database_related.db_id 36364 _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7CLS _pdbx_database_status.recvd_initial_deposition_date 2020-07-21 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Nguyen, T.Q.N.' 1 0000-0003-3837-1184 'Lim, K.W.' 2 ? 'Phan, A.T.' 3 0000-0002-4970-3861 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 48 _citation.language ? _citation.page_first 10567 _citation.page_last 10575 _citation.title 'Duplex formation in a G-quadruplex bulge.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkaa738 _citation.pdbx_database_id_PubMed 32960213 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Ngoc Nguyen, T.Q.' 1 ? primary 'Lim, K.W.' 2 ? primary 'Phan, A.T.' 3 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description 'DNA (33-MER)' _entity.formula_weight 10392.661 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;(DT)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(DC)(DA)(DG)(DA)(DT)(DG) (DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT)(DG)(DG)(DG)(DT) ; _entity_poly.pdbx_seq_one_letter_code_can TTGGATCTGAGAATCAGATGTGGGTGGGTGGGT _entity_poly.pdbx_strand_id A _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 DT n 1 2 DT n 1 3 DG n 1 4 DG n 1 5 DA n 1 6 DT n 1 7 DC n 1 8 DT n 1 9 DG n 1 10 DA n 1 11 DG n 1 12 DA n 1 13 DA n 1 14 DT n 1 15 DC n 1 16 DA n 1 17 DG n 1 18 DA n 1 19 DT n 1 20 DG n 1 21 DT n 1 22 DG n 1 23 DG n 1 24 DG n 1 25 DT n 1 26 DG n 1 27 DG n 1 28 DG n 1 29 DT n 1 30 DG n 1 31 DG n 1 32 DG n 1 33 DT 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 1 _pdbx_entity_src_syn.pdbx_end_seq_num 33 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7CLS _struct_ref.pdbx_db_accession 7CLS _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7CLS _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 33 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7CLS _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 33 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 33 # 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 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '1D proton' 2 isotropic 10 2 2 '1D proton' 2 isotropic 2 1 1 '2D JRechoNOESY 200 ms' 2 isotropic 7 2 2 '2D NOESY 100 ms' 2 isotropic 11 2 2 '2D NOESY 200 ms' 2 isotropic 3 2 2 '2D NOESY 300 ms' 2 isotropic 4 2 2 '2D HSQC-sugar' 2 isotropic 5 2 2 '2D HSQC-aromatic' 2 isotropic 6 1 3 '1D HMQC' 1 isotropic 8 2 2 '2D COSY' 2 isotropic 9 2 2 '2D TOSCY' 2 isotropic # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 298 atm 1 7.0 71.4 ? ? mM H2O 0.1 'Not defined' ? 0.5 K 2 298 atm 1 7.0 71.4 ? ? mM D2O 0.1 'Not defined' ? 0.5 K 3 298 atm 1 7.0 71.4 ? ? mM H2O_15N 0.1 'Not defined' ? 0.5 K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 '0.7 mM N.A DNA (33-MER), 30 mM N.A potassium chloride, 10.7 mM N.A K2HPO4, 9.3 mM N.A KH2PO4, 90% H2O/10% D2O' '90% H2O/10% D2O' H2O solution ? 3 '0.7 mM 15N Guanine DNA (33-MER), 30 mM N.A potassium chloride, 10.7 mM N.A K2HPO4, 9.3 mM N.A KH2PO4, 90% H2O/10% D2O' '90% H2O/10% D2O' H2O-15N solution ? 2 '0.7 mM N.A DNA (33-MER), 30 mM N.A potassium chloride, 10.7 mM N.A K2HPO4, 9.3 mM N.A KH2PO4, 100% D2O' '100% D2O' D2O solution ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 AVANCE ? Bruker 600 ? 2 AVANCE ? Bruker 700 ? # _pdbx_nmr_refine.entry_id 7CLS _pdbx_nmr_refine.method 'DGSA-distance geometry simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 7CLS _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' # _pdbx_nmr_representative.entry_id 7CLS _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal 'data analysis' Felix ? 'Accelrys Software Inc.' 1 'structure calculation' 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 2 processing TopSpin ? 'Bruker Biospin' 3 'peak picking' Felix ? 'Accelrys Software Inc.' 4 'data analysis' SpinWorks ? 'Kirk Marat' 5 refinement 'X-PLOR NIH' ? 'Schwieters, Kuszewski, Tjandra and Clore' 6 'chemical shift assignment' Felix ? 'Accelrys Software Inc.' 7 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7CLS _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7CLS _struct.title 'Solution structure of an intramolecular G-quadruplex containing a duplex bulge' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7CLS _struct_keywords.text 'G-quadruplex, DNA, quadruplex-duplex hybrid, bulge' _struct_keywords.pdbx_keywords DNA # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.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 3 N1 ? ? ? 1_555 A DG 22 O6 ? ? A DG 3 A DG 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog2 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DG 22 N7 ? ? A DG 3 A DG 22 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog3 hydrog ? ? A DG 3 N7 ? ? ? 1_555 A DG 30 N2 ? ? A DG 3 A DG 30 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog4 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DG 30 N1 ? ? A DG 3 A DG 30 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog5 hydrog ? ? A DG 4 N1 ? ? ? 1_555 A DG 23 O6 ? ? A DG 4 A DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog6 hydrog ? ? A DG 4 N2 ? ? ? 1_555 A DG 23 N7 ? ? A DG 4 A DG 23 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog7 hydrog ? ? A DG 4 N7 ? ? ? 1_555 A DG 31 N2 ? ? A DG 4 A DG 31 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog8 hydrog ? ? A DG 4 O6 ? ? ? 1_555 A DG 31 N1 ? ? A DG 4 A DG 31 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog9 hydrog ? ? A DT 6 N3 ? ? ? 1_555 A DA 18 N1 ? ? A DT 6 A DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 6 O4 ? ? ? 1_555 A DA 18 N6 ? ? A DT 6 A DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 7 N3 ? ? ? 1_555 A DG 17 N1 ? ? A DC 7 A DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 7 N4 ? ? ? 1_555 A DG 17 O6 ? ? A DC 7 A DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 7 O2 ? ? ? 1_555 A DG 17 N2 ? ? A DC 7 A DG 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 N3 ? ? ? 1_555 A DA 16 N1 ? ? A DT 8 A DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 8 O4 ? ? ? 1_555 A DA 16 N6 ? ? A DT 8 A DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 15 N3 ? ? A DG 9 A DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 15 O2 ? ? A DG 9 A DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 15 N4 ? ? A DG 9 A DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DA 10 N1 ? ? ? 1_555 A DT 14 N3 ? ? A DA 10 A DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DA 10 N6 ? ? ? 1_555 A DT 14 O4 ? ? A DA 10 A DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 20 N1 ? ? ? 1_555 A DG 24 O6 ? ? A DG 20 A DG 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog22 hydrog ? ? A DG 20 N2 ? ? ? 1_555 A DG 24 N7 ? ? A DG 20 A DG 24 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog23 hydrog ? ? A DG 20 N7 ? ? ? 1_555 A DG 32 N2 ? ? A DG 20 A DG 32 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog24 hydrog ? ? A DG 20 O6 ? ? ? 1_555 A DG 32 N1 ? ? A DG 20 A DG 32 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog25 hydrog ? ? A DG 22 N1 ? ? ? 1_555 A DG 26 O6 ? ? A DG 22 A DG 26 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog26 hydrog ? ? A DG 22 N2 ? ? ? 1_555 A DG 26 N7 ? ? A DG 22 A DG 26 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog27 hydrog ? ? A DG 23 N1 ? ? ? 1_555 A DG 27 O6 ? ? A DG 23 A DG 27 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog28 hydrog ? ? A DG 23 N2 ? ? ? 1_555 A DG 27 N7 ? ? A DG 23 A DG 27 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog29 hydrog ? ? A DG 24 N1 ? ? ? 1_555 A DG 28 O6 ? ? A DG 24 A DG 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog30 hydrog ? ? A DG 24 N2 ? ? ? 1_555 A DG 28 N7 ? ? A DG 24 A DG 28 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog31 hydrog ? ? A DG 26 N1 ? ? ? 1_555 A DG 30 O6 ? ? A DG 26 A DG 30 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog32 hydrog ? ? A DG 26 N2 ? ? ? 1_555 A DG 30 N7 ? ? A DG 26 A DG 30 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog33 hydrog ? ? A DG 27 N1 ? ? ? 1_555 A DG 31 O6 ? ? A DG 27 A DG 31 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog34 hydrog ? ? A DG 27 N2 ? ? ? 1_555 A DG 31 N7 ? ? A DG 27 A DG 31 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog35 hydrog ? ? A DG 28 N1 ? ? ? 1_555 A DG 32 O6 ? ? A DG 28 A DG 32 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? hydrog36 hydrog ? ? A DG 28 N2 ? ? ? 1_555 A DG 32 N7 ? ? A DG 28 A DG 32 1_555 ? ? ? ? ? ? TYPE_6_PAIR ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _atom_sites.entry_id 7CLS _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _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 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # 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 DT 1 1 1 DT DT A . n A 1 2 DT 2 2 2 DT DT A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DA 5 5 5 DA DA A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DA 10 10 10 DA DA A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DA 12 12 12 DA DA A . n A 1 13 DA 13 13 13 DA DA A . n A 1 14 DT 14 14 14 DT DT A . n A 1 15 DC 15 15 15 DC DC A . n A 1 16 DA 16 16 16 DA DA A . n A 1 17 DG 17 17 17 DG DG A . n A 1 18 DA 18 18 18 DA DA A . n A 1 19 DT 19 19 19 DT DT A . n A 1 20 DG 20 20 20 DG DG A . n A 1 21 DT 21 21 21 DT DT A . n A 1 22 DG 22 22 22 DG DG A . n A 1 23 DG 23 23 23 DG DG A . n A 1 24 DG 24 24 24 DG DG A . n A 1 25 DT 25 25 25 DT DT A . n A 1 26 DG 26 26 26 DG DG A . n A 1 27 DG 27 27 27 DG DG A . n A 1 28 DG 28 28 28 DG DG A . n A 1 29 DT 29 29 29 DT DT A . n A 1 30 DG 30 30 30 DG DG A . n A 1 31 DG 31 31 31 DG DG A . n A 1 32 DG 32 32 32 DG DG A . n A 1 33 DT 33 33 33 DT DT A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 ? _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 2020-09-30 2 'Structure model' 2 0 2020-10-14 3 'Structure model' 2 1 2020-10-21 4 'Structure model' 2 2 2023-06-14 # _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' Advisory 2 2 'Structure model' 'Atomic model' 3 2 'Structure model' 'Derived calculations' 4 2 'Structure model' 'Refinement description' 5 3 'Structure model' 'Database references' 6 4 'Structure model' 'Database references' 7 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 2 'Structure model' atom_site 2 2 'Structure model' ndb_struct_na_base_pair 3 2 'Structure model' ndb_struct_na_base_pair_step 4 2 'Structure model' pdbx_nmr_refine 5 2 'Structure model' pdbx_validate_close_contact 6 3 'Structure model' citation 7 4 'Structure model' database_2 8 4 'Structure model' pdbx_database_status # 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 2 'Structure model' '_atom_site.B_iso_or_equiv' 2 2 'Structure model' '_atom_site.Cartn_x' 3 2 'Structure model' '_atom_site.Cartn_y' 4 2 'Structure model' '_atom_site.Cartn_z' 5 2 'Structure model' '_ndb_struct_na_base_pair.buckle' 6 2 'Structure model' '_ndb_struct_na_base_pair.hbond_type_12' 7 2 'Structure model' '_ndb_struct_na_base_pair.hbond_type_28' 8 2 'Structure model' '_ndb_struct_na_base_pair.i_auth_seq_id' 9 2 'Structure model' '_ndb_struct_na_base_pair.i_label_comp_id' 10 2 'Structure model' '_ndb_struct_na_base_pair.i_label_seq_id' 11 2 'Structure model' '_ndb_struct_na_base_pair.j_auth_seq_id' 12 2 'Structure model' '_ndb_struct_na_base_pair.j_label_comp_id' 13 2 'Structure model' '_ndb_struct_na_base_pair.j_label_seq_id' 14 2 'Structure model' '_ndb_struct_na_base_pair.opening' 15 2 'Structure model' '_ndb_struct_na_base_pair.pair_name' 16 2 'Structure model' '_ndb_struct_na_base_pair.propeller' 17 2 'Structure model' '_ndb_struct_na_base_pair.shear' 18 2 'Structure model' '_ndb_struct_na_base_pair.stagger' 19 2 'Structure model' '_ndb_struct_na_base_pair.stretch' 20 2 'Structure model' '_ndb_struct_na_base_pair_step.helical_rise' 21 2 'Structure model' '_ndb_struct_na_base_pair_step.helical_twist' 22 2 'Structure model' '_ndb_struct_na_base_pair_step.i_auth_seq_id_1' 23 2 'Structure model' '_ndb_struct_na_base_pair_step.i_auth_seq_id_2' 24 2 'Structure model' '_ndb_struct_na_base_pair_step.i_label_comp_id_1' 25 2 'Structure model' '_ndb_struct_na_base_pair_step.i_label_comp_id_2' 26 2 'Structure model' '_ndb_struct_na_base_pair_step.i_label_seq_id_1' 27 2 'Structure model' '_ndb_struct_na_base_pair_step.i_label_seq_id_2' 28 2 'Structure model' '_ndb_struct_na_base_pair_step.inclination' 29 2 'Structure model' '_ndb_struct_na_base_pair_step.j_auth_seq_id_1' 30 2 'Structure model' '_ndb_struct_na_base_pair_step.j_auth_seq_id_2' 31 2 'Structure model' '_ndb_struct_na_base_pair_step.j_label_comp_id_1' 32 2 'Structure model' '_ndb_struct_na_base_pair_step.j_label_comp_id_2' 33 2 'Structure model' '_ndb_struct_na_base_pair_step.j_label_seq_id_1' 34 2 'Structure model' '_ndb_struct_na_base_pair_step.j_label_seq_id_2' 35 2 'Structure model' '_ndb_struct_na_base_pair_step.rise' 36 2 'Structure model' '_ndb_struct_na_base_pair_step.roll' 37 2 'Structure model' '_ndb_struct_na_base_pair_step.shift' 38 2 'Structure model' '_ndb_struct_na_base_pair_step.slide' 39 2 'Structure model' '_ndb_struct_na_base_pair_step.step_name' 40 2 'Structure model' '_ndb_struct_na_base_pair_step.tilt' 41 2 'Structure model' '_ndb_struct_na_base_pair_step.tip' 42 2 'Structure model' '_ndb_struct_na_base_pair_step.twist' 43 2 'Structure model' '_ndb_struct_na_base_pair_step.x_displacement' 44 2 'Structure model' '_ndb_struct_na_base_pair_step.y_displacement' 45 2 'Structure model' '_pdbx_validate_close_contact.PDB_model_num' 46 2 'Structure model' '_pdbx_validate_close_contact.auth_atom_id_1' 47 2 'Structure model' '_pdbx_validate_close_contact.auth_atom_id_2' 48 2 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_1' 49 2 'Structure model' '_pdbx_validate_close_contact.auth_comp_id_2' 50 2 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_1' 51 2 'Structure model' '_pdbx_validate_close_contact.auth_seq_id_2' 52 2 'Structure model' '_pdbx_validate_close_contact.dist' 53 3 'Structure model' '_citation.journal_volume' 54 3 'Structure model' '_citation.page_first' 55 3 'Structure model' '_citation.page_last' 56 4 'Structure model' '_database_2.pdbx_DOI' 57 4 'Structure model' '_database_2.pdbx_database_accession' 58 4 'Structure model' '_pdbx_database_status.status_code_nmr_data' # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 'DNA (33-MER)' 0.7 ? mM N.A 1 'potassium chloride' 30 ? mM N.A 1 K2HPO4 10.7 ? mM N.A 1 KH2PO4 9.3 ? mM N.A 3 'DNA (33-MER)' 0.7 ? mM '15N Guanine' 3 'potassium chloride' 30 ? mM N.A 3 K2HPO4 10.7 ? mM N.A 3 KH2PO4 9.3 ? mM N.A 2 'DNA (33-MER)' 0.7 ? mM N.A 2 'potassium chloride' 30 ? mM N.A 2 K2HPO4 10.7 ? mM N.A 2 KH2PO4 9.3 ? mM N.A # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 "H4'" A DT 29 ? ? OP2 A DG 31 ? ? 1.46 2 1 "HO5'" A DT 1 ? ? O6 A DG 3 ? ? 1.56 3 8 "H1'" A DG 24 ? ? OP2 A DT 25 ? ? 1.59 4 8 "H4'" A DG 24 ? ? "O5'" A DT 25 ? ? 1.60 5 10 "H4'" A DG 24 ? ? "O5'" A DT 25 ? ? 1.60 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7CLS 'double helix' 7CLS 'b-form double helix' 7CLS 'hairpin loop' 7CLS 'quadruple 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 DT 6 1_555 A DA 18 1_555 -1.068 -0.283 -1.178 11.679 11.527 -15.640 1 A_DT6:DA18_A A 6 ? A 18 ? 20 1 1 A DC 7 1_555 A DG 17 1_555 0.114 -0.294 -0.658 4.107 -5.811 -0.095 2 A_DC7:DG17_A A 7 ? A 17 ? 19 1 1 A DT 8 1_555 A DA 16 1_555 -0.008 -0.228 -0.527 -1.881 5.665 -6.314 3 A_DT8:DA16_A A 8 ? A 16 ? 20 1 1 A DG 9 1_555 A DC 15 1_555 0.351 -0.148 -0.578 -1.554 2.191 -6.352 4 A_DG9:DC15_A A 9 ? A 15 ? 19 1 1 A DA 10 1_555 A DT 14 1_555 0.893 -0.189 -0.305 6.347 17.188 -10.554 5 A_DA10:DT14_A A 10 ? A 14 ? 20 1 1 A DG 26 1_555 A DG 30 1_555 1.146 3.787 0.023 1.333 -3.993 -91.396 6 A_DG26:DG30_A A 26 ? A 30 ? 6 3 1 A DG 27 1_555 A DG 31 1_555 1.253 3.885 0.042 -6.151 -2.978 -92.160 7 A_DG27:DG31_A A 27 ? A 31 ? 6 3 1 A DG 23 1_555 A DG 4 1_555 -1.059 -3.639 0.129 -3.909 1.402 93.361 8 A_DG23:DG4_A A 23 ? A 4 ? 6 3 1 A DG 22 1_555 A DG 3 1_555 -1.370 -3.529 0.222 2.851 9.091 92.565 9 A_DG22:DG3_A A 22 ? A 3 ? 6 3 1 A DG 32 1_555 A DG 20 1_555 1.693 3.217 -0.611 2.554 5.528 -91.287 10 A_DG32:DG20_A A 32 ? A 20 ? 6 3 # 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 DT 6 1_555 A DA 18 1_555 A DC 7 1_555 A DG 17 1_555 0.942 -1.270 4.694 -0.842 -3.316 34.663 -1.391 -1.760 4.767 -5.549 1.409 34.826 1 AA_DT6DC7:DG17DA18_AA A 6 ? A 18 ? A 7 ? A 17 ? 1 A DC 7 1_555 A DG 17 1_555 A DT 8 1_555 A DA 16 1_555 -0.135 -1.551 4.687 -2.448 -8.603 31.183 -0.508 -0.404 4.925 -15.606 4.441 32.410 2 AA_DC7DT8:DA16DG17_AA A 7 ? A 17 ? A 8 ? A 16 ? 1 A DT 8 1_555 A DA 16 1_555 A DG 9 1_555 A DC 15 1_555 -0.349 -1.450 4.365 -0.602 4.911 27.105 -4.604 0.542 4.050 10.369 1.270 27.545 3 AA_DT8DG9:DC15DA16_AA A 8 ? A 16 ? A 9 ? A 15 ? 1 A DG 9 1_555 A DC 15 1_555 A DA 10 1_555 A DT 14 1_555 -0.122 -1.171 3.930 -1.593 -0.439 28.614 -2.247 -0.186 3.948 -0.888 3.219 28.660 4 AA_DG9DA10:DT14DC15_AA A 9 ? A 15 ? A 10 ? A 14 ? 1 A DG 26 1_555 A DG 30 1_555 A DG 27 1_555 A DG 31 1_555 -0.704 -0.653 3.523 -1.608 0.033 31.513 -1.207 0.971 3.552 0.060 2.958 31.553 5 AA_DG26DG27:DG31DG30_AA A 26 ? A 30 ? A 27 ? A 31 ? 1 A DG 27 1_555 A DG 31 1_555 A DG 23 1_555 A DG 4 1_555 -1.542 -3.600 -0.066 -1.647 2.760 179.841 -1.800 0.771 -0.066 1.380 0.824 179.841 6 AA_DG27DG23:DG4DG31_AA A 27 ? A 31 ? A 23 ? A 4 ? 1 A DG 23 1_555 A DG 4 1_555 A DG 22 1_555 A DG 3 1_555 -0.072 1.006 -3.498 0.463 -3.401 -29.216 -2.748 -0.245 -3.360 6.713 0.914 -29.412 7 AA_DG23DG22:DG3DG4_AA A 23 ? A 4 ? A 22 ? A 3 ? # _pdbx_audit_support.funding_organization 'National Research Foundation (NRF, Singapore)' _pdbx_audit_support.country Singapore _pdbx_audit_support.grant_number NRF-NRFI2017-09 _pdbx_audit_support.ordinal 1 # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #