data_2LFX # _entry.id 2LFX # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 2LFX pdb_00002lfx 10.2210/pdb2lfx/pdb RCSB RCSB102343 ? ? BMRB 17786 ? ? WWPDB D_1000102343 ? ? # loop_ _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.content_type _pdbx_database_related.details 17786 BMRB unspecified . 2LFY PDB unspecified . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LFX _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-07-18 _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.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Huang, H.' 1 'Das, R.S.' 2 'Basu, A.' 3 'Stone, M.P.' 4 # _citation.id primary _citation.title ;Structures of (5'S)-8,5'-Cyclo-2'-deoxyguanosine Mismatched with dA or dT. ; _citation.journal_abbrev Chem.Res.Toxicol. _citation.journal_volume 25 _citation.page_first 478 _citation.page_last 490 _citation.year 2012 _citation.journal_id_ASTM CRTOEC _citation.country US _citation.journal_id_ISSN 0893-228X _citation.journal_id_CSD 2140 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22309170 _citation.pdbx_database_id_DOI 10.1021/tx2005053 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Huang, H.' 1 ? primary 'Das, R.S.' 2 ? primary 'Basu, A.K.' 3 ? primary 'Stone, M.P.' 4 ? # 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*TP*GP*CP*(2LF)P*TP*GP*TP*TP*TP*GP*T)-3') ; 3713.394 1 ? ? ? ? 2 polymer syn ;DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*TP*GP*CP*AP*C)-3') ; 3624.409 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)(DT)(DG)(DC)(2LF)(DT)(DG)(DT)(DT)(DT)(DG)(DT)' GTGCXTGTTTGT A ? 2 polydeoxyribonucleotide no no '(DA)(DC)(DA)(DA)(DA)(DC)(DA)(DT)(DG)(DC)(DA)(DC)' ACAAACATGCAC 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 DT n 1 3 DG n 1 4 DC n 1 5 2LF n 1 6 DT n 1 7 DG n 1 8 DT n 1 9 DT n 1 10 DT n 1 11 DG n 1 12 DT n 2 1 DA n 2 2 DC n 2 3 DA n 2 4 DA n 2 5 DA n 2 6 DC n 2 7 DA n 2 8 DT n 2 9 DG n 2 10 DC n 2 11 DA n 2 12 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 2LFX 2LFX 1 ? ? ? 2 PDB 2LFX 2LFX 2 ? ? ? # 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 2LFX A 1 ? 12 ? 2LFX 1 ? 12 ? 1 12 2 2 2LFX B 1 ? 12 ? 2LFX 13 ? 24 ? 13 24 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight 2LF 'DNA linking' . '(6S,7S,8S,10R)-2-amino-8-hydroxy-4-oxo-3,6,7,8,9,10-hexahydro-4H-7,10-epoxyazepino[1,2-e]purin-6-yl dihydrogen phosphate' ? 'C10 H12 N5 O7 P' 345.205 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.conditions_id _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type 1 1 1 '2D 1H-1H NOESY' 1 2 1 '2D 1H-1H COSY' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 100 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _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 # _pdbx_nmr_sample_details.contents ;1.0 mM DNA (5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3'), 1.0 mM DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3'), 100% D2O ; _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.solvent_system '100% D2O' # _pdbx_nmr_spectrometer.field_strength 800 _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 2LFX _pdbx_nmr_refine.method 'simulated annealing' _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 'back calculated data agree with experimental NOESY spectrum' _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LFX _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 2LFX _pdbx_nmr_representative.selection_criteria 'closest to the average' # _pdbx_nmr_software.authors 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' _pdbx_nmr_software.classification refinement _pdbx_nmr_software.name Amber _pdbx_nmr_software.version 10 _pdbx_nmr_software.ordinal 1 # _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 2LFX _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LFX _struct.title ;Structure of the duplex when (5'S)-8,5'-cyclo-2'-deoxyguanosine is placed opposite dT ; _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LFX _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;(5'S)-8, 5'-cyclo-2'-deoxyguanosine, cyclopurine, cyclo-dG, DNA ; # 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 covale1 covale both ? A DC 4 "O3'" ? ? ? 1_555 A 2LF 5 P ? ? A DC 4 A 2LF 5 1_555 ? ? ? ? ? ? ? 1.611 ? ? covale2 covale both ? A 2LF 5 "O3'" ? ? ? 1_555 A DT 6 P ? ? A 2LF 5 A DT 6 1_555 ? ? ? ? ? ? ? 1.603 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 B DC 12 N3 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 B DC 12 O2 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 B DC 12 N4 ? ? A DG 1 B DC 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B DA 11 N1 ? ? A DT 2 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B DA 11 N6 ? ? A DT 2 B DA 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B DC 10 N3 ? ? A DG 3 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B DC 10 O2 ? ? A DG 3 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B DC 10 N4 ? ? A DG 3 B DC 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 B DG 9 N1 ? ? A DC 4 B DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? A DC 4 B DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DG 9 N2 ? ? A DC 4 B DG 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 6 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 6 B DA 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 7 N1 ? ? ? 1_555 B DC 6 N3 ? ? A DG 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 7 N2 ? ? ? 1_555 B DC 6 O2 ? ? A DG 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 7 O6 ? ? ? 1_555 B DC 6 N4 ? ? A DG 7 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 9 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 9 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 9 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 3 N1 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 10 O4 ? ? ? 1_555 B DA 3 N6 ? ? A DT 10 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 11 N1 ? ? ? 1_555 B DC 2 N3 ? ? A DG 11 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 11 N2 ? ? ? 1_555 B DC 2 O2 ? ? A DG 11 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 11 O6 ? ? ? 1_555 B DC 2 N4 ? ? A DG 11 B DC 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DT 12 N3 ? ? ? 1_555 B DA 1 N1 ? ? A DT 12 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DT 12 O4 ? ? ? 1_555 B DA 1 N6 ? ? A DT 12 B DA 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2LFX _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 DG5 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 DC 4 4 4 DC DC A . n A 1 5 2LF 5 5 5 2LF CDG A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DT 8 8 8 DT DT A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DG 11 11 11 DG DG A . n A 1 12 DT 12 12 12 DT DT3 A . n B 2 1 DA 1 13 13 DA DA5 B . n B 2 2 DC 2 14 14 DC DC B . n B 2 3 DA 3 15 15 DA DA B . n B 2 4 DA 4 16 16 DA DA B . n B 2 5 DA 5 17 17 DA DA B . n B 2 6 DC 6 18 18 DC DC B . n B 2 7 DA 7 19 19 DA DA B . n B 2 8 DT 8 20 20 DT DT B . n B 2 9 DG 9 21 21 DG DG B . n B 2 10 DC 10 22 22 DC DC B . n B 2 11 DA 11 23 23 DA DA B . n B 2 12 DC 12 24 24 DC DC3 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 2012-06-27 2 'Structure model' 1 1 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' 'Data collection' 2 2 'Structure model' 'Database references' 3 2 'Structure model' 'Derived calculations' 4 2 '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' database_2 2 2 'Structure model' pdbx_database_status 3 2 'Structure model' pdbx_nmr_software 4 2 'Structure model' pdbx_nmr_spectrometer 5 2 '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 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' 3 2 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 2 'Structure model' '_pdbx_nmr_software.name' 5 2 'Structure model' '_pdbx_nmr_spectrometer.model' 6 2 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # 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 ;DNA (5'-D(*GP*TP*GP*CP*TP*GP*TP*TP*TP*GP*T)-3')-1 ; 1.0 ? mM ? 1 ;DNA (5'-D(*AP*CP*AP*AP*AP*CP*AP*CP*GP*CP*AP*C)-3')-2 ; 1.0 ? mM ? 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 "O4'" A DC 4 ? ? "C1'" A DC 4 ? ? N1 A DC 4 ? ? 110.52 108.30 2.22 0.30 N 2 1 N3 A DC 4 ? ? C2 A DC 4 ? ? O2 A DC 4 ? ? 117.18 121.90 -4.72 0.70 N 3 1 "O4'" A DT 6 ? ? "C1'" A DT 6 ? ? N1 A DT 6 ? ? 110.50 108.30 2.20 0.30 N 4 1 C6 A DT 6 ? ? C5 A DT 6 ? ? C7 A DT 6 ? ? 119.20 122.90 -3.70 0.60 N 5 1 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 119.15 122.90 -3.75 0.60 N 6 1 "O4'" A DT 10 ? ? "C1'" A DT 10 ? ? N1 A DT 10 ? ? 110.59 108.30 2.29 0.30 N 7 1 C6 A DT 10 ? ? C5 A DT 10 ? ? C7 A DT 10 ? ? 119.16 122.90 -3.74 0.60 N 8 1 "O4'" A DG 11 ? ? "C1'" A DG 11 ? ? N9 A DG 11 ? ? 110.94 108.30 2.64 0.30 N 9 1 N1 A DG 11 ? ? C6 A DG 11 ? ? O6 A DG 11 ? ? 116.23 119.90 -3.67 0.60 N 10 1 "O4'" A DT 12 ? ? "C1'" A DT 12 ? ? N1 A DT 12 ? ? 110.54 108.30 2.24 0.30 N 11 1 C4 B DA 13 ? ? C5 B DA 13 ? ? C6 B DA 13 ? ? 113.47 117.00 -3.53 0.50 N 12 1 C5 B DA 13 ? ? C6 B DA 13 ? ? N1 B DA 13 ? ? 120.99 117.70 3.29 0.50 N 13 1 N1 B DA 13 ? ? C6 B DA 13 ? ? N6 B DA 13 ? ? 114.17 118.60 -4.43 0.60 N 14 1 N3 B DC 14 ? ? C2 B DC 14 ? ? O2 B DC 14 ? ? 117.27 121.90 -4.63 0.70 N 15 1 C4 B DA 15 ? ? C5 B DA 15 ? ? C6 B DA 15 ? ? 113.47 117.00 -3.53 0.50 N 16 1 C5 B DA 15 ? ? C6 B DA 15 ? ? N1 B DA 15 ? ? 121.52 117.70 3.82 0.50 N 17 1 N1 B DA 15 ? ? C6 B DA 15 ? ? N6 B DA 15 ? ? 113.82 118.60 -4.78 0.60 N 18 1 C4 B DA 16 ? ? C5 B DA 16 ? ? C6 B DA 16 ? ? 113.68 117.00 -3.32 0.50 N 19 1 C5 B DA 16 ? ? C6 B DA 16 ? ? N1 B DA 16 ? ? 121.52 117.70 3.82 0.50 N 20 1 N1 B DA 16 ? ? C6 B DA 16 ? ? N6 B DA 16 ? ? 113.96 118.60 -4.64 0.60 N 21 1 C4 B DA 17 ? ? C5 B DA 17 ? ? C6 B DA 17 ? ? 113.60 117.00 -3.40 0.50 N 22 1 C5 B DA 17 ? ? C6 B DA 17 ? ? N1 B DA 17 ? ? 121.57 117.70 3.87 0.50 N 23 1 N1 B DA 17 ? ? C6 B DA 17 ? ? N6 B DA 17 ? ? 113.87 118.60 -4.73 0.60 N 24 1 N3 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 117.40 121.90 -4.50 0.70 N 25 1 C4 B DA 19 ? ? C5 B DA 19 ? ? C6 B DA 19 ? ? 113.99 117.00 -3.01 0.50 N 26 1 C5 B DA 19 ? ? C6 B DA 19 ? ? N1 B DA 19 ? ? 121.59 117.70 3.89 0.50 N 27 1 N1 B DA 19 ? ? C6 B DA 19 ? ? N6 B DA 19 ? ? 114.37 118.60 -4.23 0.60 N 28 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 111.30 108.30 3.00 0.30 N 29 1 C6 B DT 20 ? ? C5 B DT 20 ? ? C7 B DT 20 ? ? 119.26 122.90 -3.64 0.60 N 30 1 N3 B DC 22 ? ? C2 B DC 22 ? ? O2 B DC 22 ? ? 117.46 121.90 -4.44 0.70 N 31 1 C4 B DA 23 ? ? C5 B DA 23 ? ? C6 B DA 23 ? ? 113.85 117.00 -3.15 0.50 N 32 1 C5 B DA 23 ? ? C6 B DA 23 ? ? N1 B DA 23 ? ? 121.22 117.70 3.52 0.50 N 33 1 N1 B DA 23 ? ? C6 B DA 23 ? ? N6 B DA 23 ? ? 114.19 118.60 -4.41 0.60 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 ? ? 0.051 'SIDE CHAIN' 2 1 DT A 2 ? ? 0.068 'SIDE CHAIN' 3 1 DA B 23 ? ? 0.066 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LFX 'double helix' 2LFX 'b-form double helix' 2LFX '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 12 1_555 -0.397 -0.122 0.192 4.482 10.701 2.111 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DT 2 1_555 B DA 11 1_555 -0.184 0.067 -0.216 10.340 -4.602 -4.179 2 A_DT2:DA23_B A 2 ? B 23 ? 20 1 1 A DG 3 1_555 B DC 10 1_555 -0.221 -0.089 0.161 7.135 2.590 -1.137 3 A_DG3:DC22_B A 3 ? B 22 ? 19 1 1 A DC 4 1_555 B DG 9 1_555 0.196 -0.080 -0.398 13.334 -7.288 -0.237 4 A_DC4:DG21_B A 4 ? B 21 ? 19 1 1 A DT 6 1_555 B DA 7 1_555 -0.222 0.118 -0.372 6.960 -6.249 -6.916 5 A_DT6:DA19_B A 6 ? B 19 ? 20 1 1 A DG 7 1_555 B DC 6 1_555 -0.232 -0.107 0.236 -2.060 -12.024 -1.045 6 A_DG7:DC18_B A 7 ? B 18 ? 19 1 1 A DT 8 1_555 B DA 5 1_555 -0.297 0.035 0.151 -10.425 -13.422 -3.554 7 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DT 9 1_555 B DA 4 1_555 -0.025 -0.035 -0.206 -7.764 -16.407 -1.230 8 A_DT9:DA16_B A 9 ? B 16 ? 20 1 1 A DT 10 1_555 B DA 3 1_555 -0.073 -0.005 -0.187 -4.113 -8.912 -1.956 9 A_DT10:DA15_B A 10 ? B 15 ? 20 1 1 A DG 11 1_555 B DC 2 1_555 -0.285 -0.081 0.065 -7.671 -7.649 -1.575 10 A_DG11:DC14_B A 11 ? B 14 ? 19 1 1 A DT 12 1_555 B DA 1 1_555 -0.100 -0.076 0.537 -6.642 -5.970 -0.715 11 A_DT12:DA13_B A 12 ? B 13 ? 20 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 12 1_555 A DT 2 1_555 B DA 11 1_555 -0.435 -0.663 3.313 4.800 -0.241 30.751 -1.189 1.732 3.214 -0.452 -8.983 31.115 1 AA_DG1DT2:DA23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DT 2 1_555 B DA 11 1_555 A DG 3 1_555 B DC 10 1_555 0.264 -1.014 3.294 -3.408 12.587 31.047 -3.704 -0.984 2.653 22.321 6.044 33.612 2 AA_DT2DG3:DC22DA23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DG 3 1_555 B DC 10 1_555 A DC 4 1_555 B DG 9 1_555 0.096 -0.631 3.217 5.902 5.654 30.188 -2.211 0.908 3.016 10.613 -11.080 31.250 3 AA_DG3DC4:DG21DC22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DC 4 1_555 B DG 9 1_555 A DT 6 1_555 B DA 7 1_555 -0.984 -0.546 6.818 -6.766 17.719 70.195 -1.690 0.365 6.602 15.135 5.779 72.394 4 AA_DC4DT6:DA19DG21_BB A 4 ? B 21 ? A 6 ? B 19 ? 1 A DT 6 1_555 B DA 7 1_555 A DG 7 1_555 B DC 6 1_555 0.318 -1.142 3.608 -3.975 4.774 32.432 -2.878 -1.284 3.349 8.450 7.037 33.006 5 AA_DT6DG7:DC18DA19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DG 7 1_555 B DC 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.405 -1.061 3.494 1.704 -1.553 35.205 -1.503 0.940 3.514 -2.564 -2.813 35.278 6 AA_DG7DT8:DA17DC18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DT 9 1_555 B DA 4 1_555 0.402 -0.391 3.252 1.645 -0.947 36.905 -0.490 -0.414 3.275 -1.494 -2.596 36.952 7 AA_DT8DT9:DA16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DT 9 1_555 B DA 4 1_555 A DT 10 1_555 B DA 3 1_555 0.070 -0.799 3.353 -1.256 1.356 31.777 -1.708 -0.362 3.311 2.473 2.292 31.830 8 AA_DT9DT10:DA15DA16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DT 10 1_555 B DA 3 1_555 A DG 11 1_555 B DC 2 1_555 0.016 -0.945 3.387 -1.793 9.848 30.801 -3.425 -0.343 2.947 17.956 3.270 32.349 9 AA_DT10DG11:DC14DA15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DG 11 1_555 B DC 2 1_555 A DT 12 1_555 B DA 1 1_555 0.173 -1.150 3.474 -3.865 -0.085 32.830 -2.006 -0.997 3.435 -0.150 6.809 33.050 10 AA_DG11DT12:DA13DC14_BB A 11 ? B 14 ? A 12 ? B 13 ? #