data_2KH1 # _entry.id 2KH1 # _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 2KH1 pdb_00002kh1 10.2210/pdb2kh1/pdb RCSB RCSB101110 ? ? WWPDB D_1000101110 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2KGZ unspecified . PDB 2KH0 unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2KH1 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-03-23 _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code REL _pdbx_database_status.status_code_mr REL _pdbx_database_status.status_code_sf ? _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 'Dallmann, A.' 1 'Pfaffe, M.' 2 'Muegge, C.' 3 'Mahrwald, R.' 4 'Kovalenko, S.A.' 5 'Ernsting, N.P.' 6 # _citation.id primary _citation.title 'Local THz Time Domain Spectroscopy of Duplex DNA via Fluorescence of an Embedded Probe.' _citation.journal_abbrev J.Phys.Chem.B _citation.journal_volume 113 _citation.page_first 15619 _citation.page_last 15628 _citation.year 2009 _citation.journal_id_ASTM JPCBFK _citation.country US _citation.journal_id_ISSN 1089-5647 _citation.journal_id_CSD 1278 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19764701 _citation.pdbx_database_id_DOI 10.1021/jp906037g # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Dallmann, A.' 1 ? primary 'Pfaffe, M.' 2 ? primary 'Mahrwald, R.' 3 ? primary 'Kovalenko, S.A.' 4 ? primary 'Ernsting, N.P.' 5 ? # _cell.entry_id 2KH1 _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 2KH1 _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 "5'-D(*GP*CP*TP*GP*CP*AP*(3DR)P*AP*CP*GP*TP*CP*G)-3'" 3843.488 1 ? ? ? ? 2 polymer syn "5'-D(*CP*GP*AP*CP*GP*TP*(3DR)P*TP*GP*CP*AP*GP*C)-3'" 3843.488 1 ? ? ? ? 3 non-polymer syn 7-nitro-9H-fluoren-2-ol 227.215 1 ? ? ? ? # 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)(DG)(DC)(DA)(3DR)(DA)(DC)(DG)(DT)(DC)(DG)' GCTGCANACGTCG A ? 2 polydeoxyribonucleotide no yes '(DC)(DG)(DA)(DC)(DG)(DT)(3DR)(DT)(DG)(DC)(DA)(DG)(DC)' CGACGTNTGCAGC 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 DG n 1 5 DC n 1 6 DA n 1 7 3DR n 1 8 DA n 1 9 DC n 1 10 DG n 1 11 DT n 1 12 DC n 1 13 DG n 2 1 DC n 2 2 DG n 2 3 DA n 2 4 DC n 2 5 DG n 2 6 DT n 2 7 3DR n 2 8 DT n 2 9 DG n 2 10 DC n 2 11 DA n 2 12 DG n 2 13 DC n # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 2KH1 2KH1 1 1 GCTGCANACGTCG ? 2 PDB 2KH1 2KH1 2 1 CGACGTNTGCAGC ? # 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 2KH1 A 1 ? 13 ? 2KH1 1 ? 13 ? 1 13 2 2 2KH1 B 1 ? 13 ? 2KH1 14 ? 26 ? 14 26 # 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 3DR 'DNA linking' . "1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE" 'ABASIC DIDEOXYRIBOSE' 'C5 H11 O6 P' 198.111 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 HNF non-polymer . 7-nitro-9H-fluoren-2-ol 2-hydroxy-7-nitrofluorene 'C13 H9 N O3' 227.215 # loop_ _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 2 '2D 1H-1H COSY' 1 2 2 '2D 1H-1H NOESY' 1 3 3 '2D 1H-1H NOESY' 1 4 2 '2D 1H-13C HSQC' 1 5 2 '2D 1H-13C HSQC_decoupled' 1 6 1 '2D 1H-13C HSQC_decoupled' 1 7 2 '2D 1H-1H TOCSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.pressure ambient _pdbx_nmr_exptl_sample_conditions.pressure_units ? _pdbx_nmr_exptl_sample_conditions.temperature 298 _pdbx_nmr_exptl_sample_conditions.temperature_units K # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system '3 mM Strand I-1, 3 mM Strand II-2, 20 mg/mL Pf1 phage-3, 10 mM sodium phosphate-4, 150 mM sodium chloride-5, 100% D2O' 1 '100% D2O' '3 mM Strand I-6, 3 mM Strand II-7, 10 mM sodium phosphate-8, 150 mM sodium chloride-9, 100% D2O' 2 '100% D2O' '3 mM Strand I-10, 3 mM Strand II-11, 10 mM sodium phosphate-12, 150 mM sodium chloride-13, 90% H2O/10% D2O' 3 '90% H2O/10% D2O' # _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.type 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2KH1 _pdbx_nmr_refine.method 'simulated annealing, torsion angle dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 11 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2KH1 _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.entry_id 2KH1 _pdbx_nmr_representative.selection_criteria 'minimized average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal Delsuc 'data analysis' Gifa 4 1 'Schwieters, Kuszewski, Tjandra and Clore' 'geometry optimization' 'X-PLOR NIH' 2.20 2 'Schwieters, Kuszewski, Tjandra and Clore' refinement 'X-PLOR NIH' 2.20 3 'Schwieters, Kuszewski, Tjandra and Clore' 'structure solution' 'X-PLOR NIH' 2.20 4 'Rochus T. Keller' 'data analysis' CARA 1.8.4 5 'Rochus T. Keller' 'peak picking' CARA 1.8.4 6 'Bruker Biospin' collection TopSpin 2.1 7 'Bruker Biospin' processing TopSpin 2.1 8 # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.crystals_number ? _exptl.details ? _exptl.entry_id 2KH1 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2KH1 _struct.title '2-Hydroxy-7-nitrofluorene covalently linked into a 13mer DNA duplex - solution structure of the face-up orientation' _struct.pdbx_model_details 'minimized average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2KH1 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DNA, solution structure, base pair mimic, conformational flexibility' # 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 ? C N N 3 ? # _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 covale1 covale both ? A DA 6 "O3'" ? ? ? 1_555 A 3DR 7 P ? ? A DA 6 A 3DR 7 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale2 covale both ? A 3DR 7 "O3'" ? ? ? 1_555 A DA 8 P ? ? A 3DR 7 A DA 8 1_555 ? ? ? ? ? ? ? 1.609 ? ? covale3 covale one ? A 3DR 7 "C1'" ? ? ? 1_555 C HNF . O1 ? ? A 3DR 7 A HNF 27 1_555 ? ? ? ? ? ? ? 1.420 ? ? covale4 covale both ? B DT 6 "O3'" ? ? ? 1_555 B 3DR 7 P ? ? B DT 19 B 3DR 20 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale5 covale both ? B 3DR 7 "O3'" ? ? ? 1_555 B DT 8 P ? ? B 3DR 20 B DT 21 1_555 ? ? ? ? ? ? ? 1.609 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 13 N3 ? ? A DG 1 B DC 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 13 O2 ? ? A DG 1 B DC 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 13 N4 ? ? A DG 1 B DC 26 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 2 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 2 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 2 B DG 25 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 11 N1 ? ? A DT 3 B DA 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 11 N6 ? ? A DT 3 B DA 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 4 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 4 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 4 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 5 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 5 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 5 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 6 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 6 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 8 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 8 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 5 N1 ? ? A DC 9 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 5 O6 ? ? A DC 9 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 5 N2 ? ? A DC 9 B DG 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 4 N3 ? ? A DG 10 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 10 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 4 N4 ? ? A DG 10 B DC 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DT 11 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 11 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 11 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 11 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 12 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 12 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 12 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 13 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 13 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 13 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 13 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id HNF _struct_site.pdbx_auth_seq_id 27 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 6 _struct_site.details 'BINDING SITE FOR RESIDUE HNF A 27' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 6 3DR A 7 ? 3DR A 7 . ? 1_555 ? 3 AC1 6 DA A 8 ? DA A 8 . ? 1_555 ? 4 AC1 6 DT B 6 ? DT B 19 . ? 1_555 ? 5 AC1 6 3DR B 7 ? 3DR B 20 . ? 1_555 ? 6 AC1 6 DT B 8 ? DT B 21 . ? 1_555 ? # _atom_sites.entry_id 2KH1 _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 DG 1 1 1 DG DG A . n A 1 2 DC 2 2 2 DC DC A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 3DR 7 7 7 3DR 3DR A . n A 1 8 DA 8 8 8 DA DA A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DT 11 11 11 DT DT A . n A 1 12 DC 12 12 12 DC DC A . n A 1 13 DG 13 13 13 DG DG A . n B 2 1 DC 1 14 14 DC DC B . n B 2 2 DG 2 15 15 DG DG B . n B 2 3 DA 3 16 16 DA DA B . n B 2 4 DC 4 17 17 DC DC B . n B 2 5 DG 5 18 18 DG DG B . n B 2 6 DT 6 19 19 DT DT B . n B 2 7 3DR 7 20 20 3DR 3DR B . n B 2 8 DT 8 21 21 DT DT B . n B 2 9 DG 9 22 22 DG DG B . n B 2 10 DC 10 23 23 DC DC B . n B 2 11 DA 11 24 24 DA DA B . n B 2 12 DG 12 25 25 DG DG B . n B 2 13 DC 13 26 26 DC DC B . n # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id HNF _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 27 _pdbx_nonpoly_scheme.auth_seq_num 27 _pdbx_nonpoly_scheme.pdb_mon_id HNF _pdbx_nonpoly_scheme.auth_mon_id HNF _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _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,C # _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 2009-12-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2022-03-16 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 3 'Structure model' database_2 2 3 'Structure model' pdbx_nmr_software 3 3 'Structure model' pdbx_nmr_spectrometer 4 3 'Structure model' pdbx_struct_assembly 5 3 'Structure model' pdbx_struct_oper_list 6 3 'Structure model' struct_conn 7 3 'Structure model' struct_site # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_nmr_software.name' 4 3 'Structure model' '_pdbx_nmr_spectrometer.model' 5 3 'Structure model' '_struct_conn.pdbx_dist_value' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 7 3 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 8 3 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 9 3 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 10 3 'Structure model' '_struct_conn.ptnr1_label_asym_id' 11 3 'Structure model' '_struct_conn.ptnr1_label_atom_id' 12 3 'Structure model' '_struct_conn.ptnr1_label_comp_id' 13 3 'Structure model' '_struct_conn.ptnr1_label_seq_id' 14 3 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 15 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 16 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 17 3 'Structure model' '_struct_conn.ptnr2_label_asym_id' 18 3 'Structure model' '_struct_conn.ptnr2_label_atom_id' 19 3 'Structure model' '_struct_conn.ptnr2_label_comp_id' 20 3 'Structure model' '_struct_conn.ptnr2_label_seq_id' 21 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 22 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 23 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _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 _pdbx_nmr_exptl_sample.solution_id 'Strand I-1' 3 ? mM ? 1 'Strand II-2' 3 ? mM ? 1 'Pf1 phage-3' 20 ? mg/mL ? 1 'sodium phosphate-4' 10 ? mM ? 1 'sodium chloride-5' 150 ? mM ? 1 'Strand I-6' 3 ? mM ? 2 'Strand II-7' 3 ? mM ? 2 'sodium phosphate-8' 10 ? mM ? 2 'sodium chloride-9' 150 ? mM ? 2 'Strand I-10' 3 ? mM ? 3 'Strand II-11' 3 ? mM ? 3 'sodium phosphate-12' 10 ? mM ? 3 'sodium chloride-13' 150 ? mM ? 3 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2KH1 _pdbx_nmr_constraints.hydrogen_bond_constraints_total_count ? _pdbx_nmr_constraints.NA_alpha-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_beta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_chi-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_delta-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_epsilon-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_gamma-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_other-angle_constraints_total_count ? _pdbx_nmr_constraints.NA_sugar_pucker_constraints_total_count ? _pdbx_nmr_constraints.NOE_constraints_total 401 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count ? _pdbx_nmr_constraints.NOE_long_range_total_count ? _pdbx_nmr_constraints.NOE_medium_range_total_count ? _pdbx_nmr_constraints.NOE_motional_averaging_correction ? _pdbx_nmr_constraints.NOE_pseudoatom_corrections ? _pdbx_nmr_constraints.NOE_sequential_total_count ? _pdbx_nmr_constraints.protein_chi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_other_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_phi_angle_constraints_total_count ? _pdbx_nmr_constraints.protein_psi_angle_constraints_total_count ? # 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 H22 A DG 10 ? ? O2 B DC 17 ? ? 1.60 2 1 H22 A DG 1 ? ? O2 B DC 26 ? ? 1.60 3 1 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 4 1 O2 A DC 5 ? ? H22 B DG 22 ? ? 1.60 5 2 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 6 2 H22 A DG 1 ? ? O2 B DC 26 ? ? 1.60 7 2 O2 A DC 5 ? ? H22 B DG 22 ? ? 1.60 8 3 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 9 3 H22 A DG 1 ? ? O2 B DC 26 ? ? 1.60 10 3 O2 A DC 2 ? ? H22 B DG 25 ? ? 1.60 11 5 H22 A DG 1 ? ? O2 B DC 26 ? ? 1.60 12 5 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 13 5 H22 A DG 10 ? ? O2 B DC 17 ? ? 1.60 14 6 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 15 6 O2 A DC 2 ? ? H22 B DG 25 ? ? 1.60 16 7 O2 A DC 5 ? ? H22 B DG 22 ? ? 1.60 17 7 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 18 7 H22 A DG 1 ? ? O2 B DC 26 ? ? 1.60 19 8 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 20 8 O2 A DC 2 ? ? H22 B DG 25 ? ? 1.60 21 9 H22 A DG 4 ? ? O2 B DC 23 ? ? 1.60 22 9 H22 A DG 1 ? ? O2 B DC 26 ? ? 1.60 23 9 H22 A DG 10 ? ? O2 B DC 17 ? ? 1.60 24 9 O2 A DC 5 ? ? H22 B DG 22 ? ? 1.60 25 10 O2 A DC 2 ? ? H22 B DG 25 ? ? 1.60 26 11 H22 A DG 10 ? ? O2 B DC 17 ? ? 1.60 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2KH1 'double helix' 2KH1 'b-form double helix' 2KH1 'mismatched base pair' # 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 13 1_555 -0.402 -0.263 0.066 -4.400 -5.563 1.522 1 A_DG1:DC26_B A 1 ? B 26 ? 19 1 1 A DC 2 1_555 B DG 12 1_555 0.315 -0.295 0.419 -8.067 -5.464 0.431 2 A_DC2:DG25_B A 2 ? B 25 ? 19 1 1 A DT 3 1_555 B DA 11 1_555 -0.047 -0.274 0.014 0.589 -10.147 -3.060 3 A_DT3:DA24_B A 3 ? B 24 ? 20 1 1 A DG 4 1_555 B DC 10 1_555 -0.341 -0.295 0.169 -3.420 -9.770 0.789 4 A_DG4:DC23_B A 4 ? B 23 ? 19 1 1 A DC 5 1_555 B DG 9 1_555 0.379 -0.269 0.137 -3.264 -5.519 1.385 5 A_DC5:DG22_B A 5 ? B 22 ? 19 1 1 A DA 6 1_555 B DT 8 1_555 0.019 -0.294 -0.394 4.907 16.987 -3.162 6 A_DA6:DT21_B A 6 ? B 21 ? 20 1 1 A DA 8 1_555 B DT 6 1_555 0.193 -0.267 0.004 10.801 -3.010 -4.965 7 A_DA8:DT19_B A 8 ? B 19 ? 20 1 1 A DC 9 1_555 B DG 5 1_555 0.416 -0.302 0.099 12.116 -22.725 2.512 8 A_DC9:DG18_B A 9 ? B 18 ? 19 1 1 A DG 10 1_555 B DC 4 1_555 -0.406 -0.262 -0.088 -11.252 -10.448 1.759 9 A_DG10:DC17_B A 10 ? B 17 ? 19 1 1 A DT 11 1_555 B DA 3 1_555 -0.088 -0.230 -0.059 2.650 -9.188 -4.295 10 A_DT11:DA16_B A 11 ? B 16 ? 20 1 1 A DC 12 1_555 B DG 2 1_555 0.398 -0.294 -0.239 10.634 -17.591 3.440 11 A_DC12:DG15_B A 12 ? B 15 ? 19 1 1 A DG 13 1_555 B DC 1 1_555 -0.397 -0.272 -0.241 -14.882 -15.852 2.460 12 A_DG13:DC14_B A 13 ? B 14 ? 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 13 1_555 A DC 2 1_555 B DG 12 1_555 -0.214 -0.438 3.221 -2.196 -1.873 42.456 -0.416 0.075 3.243 -2.583 3.028 42.549 1 AA_DG1DC2:DG25DC26_BB A 1 ? B 26 ? A 2 ? B 25 ? 1 A DC 2 1_555 B DG 12 1_555 A DT 3 1_555 B DA 11 1_555 -0.041 0.171 2.829 3.870 -1.817 36.998 0.476 0.507 2.799 -2.851 -6.074 37.236 2 AA_DC2DT3:DA24DG25_BB A 2 ? B 25 ? A 3 ? B 24 ? 1 A DT 3 1_555 B DA 11 1_555 A DG 4 1_555 B DC 10 1_555 0.204 -0.576 2.961 -1.458 9.004 34.603 -2.085 -0.518 2.720 14.821 2.400 35.749 3 AA_DT3DG4:DC23DA24_BB A 3 ? B 24 ? A 4 ? B 23 ? 1 A DG 4 1_555 B DC 10 1_555 A DC 5 1_555 B DG 9 1_555 0.062 -0.011 3.111 -0.108 -3.207 43.352 0.280 -0.094 3.104 -4.335 0.146 43.465 4 AA_DG4DC5:DG22DC23_BB A 4 ? B 23 ? A 5 ? B 22 ? 1 A DC 5 1_555 B DG 9 1_555 A DA 6 1_555 B DT 8 1_555 0.468 -0.737 3.054 1.577 -5.174 35.104 -0.488 -0.548 3.145 -8.515 -2.596 35.505 5 AA_DC5DA6:DT21DG22_BB A 5 ? B 22 ? A 6 ? B 21 ? 1 A DA 6 1_555 B DT 8 1_555 A DA 8 1_555 B DT 6 1_555 -1.522 0.031 5.969 3.110 15.053 54.461 -1.513 1.929 5.707 16.092 -3.325 56.429 6 AA_DA6DA8:DT19DT21_BB A 6 ? B 21 ? A 8 ? B 19 ? 1 A DA 8 1_555 B DT 6 1_555 A DC 9 1_555 B DG 5 1_555 0.403 -0.280 3.224 0.978 -11.644 42.152 0.740 -0.449 3.197 -15.828 -1.330 43.670 7 AA_DA8DC9:DG18DT19_BB A 8 ? B 19 ? A 9 ? B 18 ? 1 A DC 9 1_555 B DG 5 1_555 A DG 10 1_555 B DC 4 1_555 0.074 -1.171 3.331 1.041 12.181 33.145 -3.666 0.026 2.746 20.505 -1.752 35.268 8 AA_DC9DG10:DC17DG18_BB A 9 ? B 18 ? A 10 ? B 17 ? 1 A DG 10 1_555 B DC 4 1_555 A DT 11 1_555 B DA 3 1_555 -0.288 0.296 2.745 0.070 -4.356 39.426 0.861 0.432 2.698 -6.433 -0.104 39.656 9 AA_DG10DT11:DA16DC17_BB A 10 ? B 17 ? A 11 ? B 16 ? 1 A DT 11 1_555 B DA 3 1_555 A DC 12 1_555 B DG 2 1_555 0.505 0.296 2.793 2.878 0.009 41.465 0.417 -0.450 2.820 0.013 -4.058 41.560 10 AA_DT11DC12:DG15DA16_BB A 11 ? B 16 ? A 12 ? B 15 ? 1 A DC 12 1_555 B DG 2 1_555 A DG 13 1_555 B DC 1 1_555 -0.043 -1.114 3.354 0.460 19.683 31.412 -4.252 0.127 2.287 32.652 -0.763 36.940 11 AA_DC12DG13:DC14DG15_BB A 12 ? B 15 ? A 13 ? B 14 ? # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 7-nitro-9H-fluoren-2-ol _pdbx_entity_nonpoly.comp_id HNF #