data_2LIA # _entry.id 2LIA # _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 2LIA pdb_00002lia 10.2210/pdb2lia/pdb RCSB RCSB102418 ? ? BMRB 17885 ? ? WWPDB D_1000102418 ? ? # _pdbx_database_related.db_id 17885 _pdbx_database_related.db_name BMRB _pdbx_database_related.content_type unspecified _pdbx_database_related.details . # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LIA _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-08-26 _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 'Szulik, M.W.' 1 'Ganguly, M.' 2 'Wang, R.' 3 'Gold, B.' 4 'Stone, M.P.' 5 # _citation.id primary _citation.title ;Site-Specific Stabilization of DNA by a Tethered Major Groove Amine, 7-Aminomethyl-7-deaza-2'-deoxyguanosine. ; _citation.journal_abbrev Biochemistry _citation.journal_volume 52 _citation.page_first 7659 _citation.page_last 7668 _citation.year 2013 _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 24131376 _citation.pdbx_database_id_DOI 10.1021/bi400695r # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Szulik, M.W.' 1 ? primary 'Voehler, M.W.' 2 ? primary 'Ganguly, M.' 3 ? primary 'Gold, B.' 4 ? primary 'Stone, M.P.' 5 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*GP*AP*GP*AP*(2LA)P*CP*GP*CP*TP*CP*TP*C)-3') ; _entity.formula_weight 3691.445 _entity.pdbx_number_of_molecules 2 _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 yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DA)(DG)(DA)(2LA)(DC)(DG)(DC)(DT)(DC)(DT)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GAGAXCGCTCTC _entity_poly.pdbx_strand_id A,B _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 DG n 1 2 DA n 1 3 DG n 1 4 DA n 1 5 2LA n 1 6 DC n 1 7 DG n 1 8 DC n 1 9 DT n 1 10 DC n 1 11 DT n 1 12 DC n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 2LIA _struct_ref.pdbx_db_accession 2LIA _struct_ref.entity_id 1 _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 2LIA A 1 ? 12 ? 2LIA 1 ? 12 ? 1 12 2 1 2LIA B 1 ? 12 ? 2LIA 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 2LA 'DNA linking' . '2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one' ? 'C12 H18 N5 O7 P' 375.274 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 0.21 _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 # _pdbx_nmr_sample_details.contents ;0.25 mM [U-2H] DNA dodecamer, 10 mM [U-2H] sodium phosphate, 200 mM [U-2H] sodium chloride, 0.011 M [U-2H] sodium azide, 0.05 mM [U-2H] sodium EDTA, 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 2LIA _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 42 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.entry_id 2LIA _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 2LIA _pdbx_nmr_representative.selection_criteria 'closest to the average' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Bruker Biospin' processing TopSpin 2.0.b.6 1 Goddard 'chemical shift assignment' Sparky ? 2 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' refinement Amber 10 3 # _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 2LIA _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LIA _struct.title ;Solution NMR structure of a DNA dodecamer containing the 7-aminomethyl-7-deaza-2'-deoxyguanosine adduct ; _struct.pdbx_model_details 'closest to the average, model 1' _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LIA _struct_keywords.pdbx_keywords DNA _struct_keywords.text 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 1 ? # _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 4 "O3'" ? ? ? 1_555 A 2LA 5 P ? ? A DA 4 A 2LA 5 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale2 covale both ? A 2LA 5 "O3'" ? ? ? 1_555 A DC 6 P ? ? A 2LA 5 A DC 6 1_555 ? ? ? ? ? ? ? 1.620 ? ? covale3 covale both ? B DA 4 "O3'" ? ? ? 1_555 B 2LA 5 P ? ? B DA 16 B 2LA 17 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale4 covale both ? B 2LA 5 "O3'" ? ? ? 1_555 B DC 6 P ? ? B 2LA 17 B DC 18 1_555 ? ? ? ? ? ? ? 1.612 ? ? 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 DA 2 N1 ? ? ? 1_555 B DT 11 N3 ? ? A DA 2 B DT 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DA 2 N6 ? ? ? 1_555 B DT 11 O4 ? ? A DA 2 B DT 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 DA 4 N1 ? ? ? 1_555 B DT 9 N3 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 9 O4 ? ? A DA 4 B DT 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 6 N3 ? ? ? 1_555 B DG 7 N1 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 6 N4 ? ? ? 1_555 B DG 7 O6 ? ? A DC 6 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 O2 ? ? ? 1_555 B DG 7 N2 ? ? A DC 6 B DG 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 9 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 9 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 9 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 9 B DA 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B DG 3 N1 ? ? A DC 10 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B DG 3 O6 ? ? A DC 10 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B DG 3 N2 ? ? A DC 10 B DG 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 11 N3 ? ? ? 1_555 B DA 2 N1 ? ? A DT 11 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DT 11 O4 ? ? ? 1_555 B DA 2 N6 ? ? A DT 11 B DA 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 12 N3 ? ? ? 1_555 B DG 1 N1 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 12 N4 ? ? ? 1_555 B DG 1 O6 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 12 O2 ? ? ? 1_555 B DG 1 N2 ? ? A DC 12 B DG 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2LIA _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 DA 2 2 2 DA DA A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 2LA 5 5 5 2LA AMG A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DG 7 7 7 DG DG A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DT 9 9 9 DT DT A . n A 1 10 DC 10 10 10 DC DC A . n A 1 11 DT 11 11 11 DT DT A . n A 1 12 DC 12 12 12 DC DC A . n B 1 1 DG 1 13 13 DG DG5 B . n B 1 2 DA 2 14 14 DA DA B . n B 1 3 DG 3 15 15 DG DG B . n B 1 4 DA 4 16 16 DA DA B . n B 1 5 2LA 5 17 17 2LA AMG B . n B 1 6 DC 6 18 18 DC DC B . n B 1 7 DG 7 19 19 DG DG B . n B 1 8 DC 8 20 20 DC DC B . n B 1 9 DT 9 21 21 DT DT B . n B 1 10 DC 10 22 22 DC DC B . n B 1 11 DT 11 23 23 DT DT B . n B 1 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 2012-08-29 2 'Structure model' 1 1 2013-11-20 3 'Structure model' 1 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' 'Database references' 2 3 'Structure model' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' 5 3 '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 3 'Structure model' database_2 2 3 'Structure model' pdbx_database_status 3 3 'Structure model' pdbx_nmr_software 4 3 'Structure model' pdbx_nmr_spectrometer 5 3 '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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' 4 3 'Structure model' '_pdbx_nmr_software.name' 5 3 'Structure model' '_pdbx_nmr_spectrometer.model' 6 3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # _pdbx_nmr_ensemble_rms.atom_type ? _pdbx_nmr_ensemble_rms.bond_angle_rms_dev ? _pdbx_nmr_ensemble_rms.bond_angle_rms_dev_error ? _pdbx_nmr_ensemble_rms.chain_range_begin ? _pdbx_nmr_ensemble_rms.chain_range_end ? _pdbx_nmr_ensemble_rms.coord_average_rmsd_method ? _pdbx_nmr_ensemble_rms.covalent_bond_rms_dev ? _pdbx_nmr_ensemble_rms.covalent_bond_rms_dev_error ? _pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev ? _pdbx_nmr_ensemble_rms.dihedral_angles_rms_dev_error ? _pdbx_nmr_ensemble_rms.distance_rms_dev 0.453 _pdbx_nmr_ensemble_rms.distance_rms_dev_error ? _pdbx_nmr_ensemble_rms.entry_id 2LIA _pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev ? _pdbx_nmr_ensemble_rms.improper_torsion_angle_rms_dev_error ? _pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev ? _pdbx_nmr_ensemble_rms.peptide_planarity_rms_dev_error ? _pdbx_nmr_ensemble_rms.residue_range_begin ? _pdbx_nmr_ensemble_rms.residue_range_end ? # 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 dodecamer-1' 0.25 ? mM '[U-2H]' 1 'sodium phosphate-2' 10 ? mM '[U-2H]' 1 'sodium chloride-3' 200 ? mM '[U-2H]' 1 'sodium azide-4' 0.011 ? M '[U-2H]' 1 'sodium EDTA-5' 0.05 ? mM '[U-2H]' 1 # _pdbx_nmr_constraints.disulfide_bond_constraints_total_count ? _pdbx_nmr_constraints.entry_id 2LIA _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 211 _pdbx_nmr_constraints.NOE_interentity_total_count ? _pdbx_nmr_constraints.NOE_interproton_distance_evaluation ? _pdbx_nmr_constraints.NOE_intraresidue_total_count 114 _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 97 _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_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 ? ? 111.30 108.30 3.00 0.30 N 2 1 "O4'" A DA 2 ? ? "C1'" A DA 2 ? ? N9 A DA 2 ? ? 112.33 108.30 4.03 0.30 N 3 1 C4 A DA 2 ? ? C5 A DA 2 ? ? C6 A DA 2 ? ? 113.45 117.00 -3.55 0.50 N 4 1 C5 A DA 2 ? ? C6 A DA 2 ? ? N1 A DA 2 ? ? 122.26 117.70 4.56 0.50 N 5 1 N1 A DA 2 ? ? C6 A DA 2 ? ? N6 A DA 2 ? ? 113.18 118.60 -5.42 0.60 N 6 1 "O4'" A DC 6 ? ? "C1'" A DC 6 ? ? N1 A DC 6 ? ? 110.37 108.30 2.07 0.30 N 7 1 N1 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 123.84 118.90 4.94 0.60 N 8 1 N3 A DC 6 ? ? C2 A DC 6 ? ? O2 A DC 6 ? ? 115.87 121.90 -6.03 0.70 N 9 1 "O4'" A DG 7 ? ? "C1'" A DG 7 ? ? N9 A DG 7 ? ? 110.21 108.30 1.91 0.30 N 10 1 N3 A DC 8 ? ? C4 A DC 8 ? ? C5 A DC 8 ? ? 124.42 121.90 2.52 0.40 N 11 1 N3 A DC 8 ? ? C2 A DC 8 ? ? O2 A DC 8 ? ? 116.97 121.90 -4.93 0.70 N 12 1 N3 A DC 8 ? ? C4 A DC 8 ? ? N4 A DC 8 ? ? 112.90 118.00 -5.10 0.70 N 13 1 "O4'" A DT 9 ? ? "C1'" A DT 9 ? ? N1 A DT 9 ? ? 110.25 108.30 1.95 0.30 N 14 1 C6 A DT 9 ? ? C5 A DT 9 ? ? C7 A DT 9 ? ? 118.03 122.90 -4.87 0.60 N 15 1 "O4'" A DC 10 ? ? "C4'" A DC 10 ? ? "C3'" A DC 10 ? ? 109.75 106.00 3.75 0.60 N 16 1 N3 A DC 10 ? ? C2 A DC 10 ? ? O2 A DC 10 ? ? 117.53 121.90 -4.37 0.70 N 17 1 "O4'" A DT 11 ? ? "C1'" A DT 11 ? ? N1 A DT 11 ? ? 110.76 108.30 2.46 0.30 N 18 1 "O4'" A DC 12 ? ? "C1'" A DC 12 ? ? N1 A DC 12 ? ? 112.15 108.30 3.85 0.30 N 19 1 N1 A DC 12 ? ? C2 A DC 12 ? ? O2 A DC 12 ? ? 122.81 118.90 3.91 0.60 N 20 1 N3 A DC 12 ? ? C2 A DC 12 ? ? O2 A DC 12 ? ? 116.35 121.90 -5.55 0.70 N 21 1 "O4'" B DA 14 ? ? "C1'" B DA 14 ? ? N9 B DA 14 ? ? 110.75 108.30 2.45 0.30 N 22 1 N1 B DA 14 ? ? C6 B DA 14 ? ? N6 B DA 14 ? ? 114.08 118.60 -4.52 0.60 N 23 1 "O4'" B DG 15 ? ? "C1'" B DG 15 ? ? N9 B DG 15 ? ? 112.11 108.30 3.81 0.30 N 24 1 N1 B DG 15 ? ? C6 B DG 15 ? ? O6 B DG 15 ? ? 116.01 119.90 -3.89 0.60 N 25 1 C4 B DA 16 ? ? C5 B DA 16 ? ? C6 B DA 16 ? ? 113.97 117.00 -3.03 0.50 N 26 1 C5 B DA 16 ? ? C6 B DA 16 ? ? N1 B DA 16 ? ? 121.28 117.70 3.58 0.50 N 27 1 N1 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 123.25 118.90 4.35 0.60 N 28 1 N3 B DC 18 ? ? C2 B DC 18 ? ? O2 B DC 18 ? ? 116.67 121.90 -5.23 0.70 N 29 1 N3 B DC 20 ? ? C2 B DC 20 ? ? O2 B DC 20 ? ? 116.97 121.90 -4.93 0.70 N 30 1 C6 B DT 21 ? ? C5 B DT 21 ? ? C7 B DT 21 ? ? 116.92 122.90 -5.98 0.60 N 31 1 N3 B DC 22 ? ? C2 B DC 22 ? ? O2 B DC 22 ? ? 117.26 121.90 -4.64 0.70 N 32 1 "O4'" B DT 23 ? ? "C1'" B DT 23 ? ? N1 B DT 23 ? ? 112.70 108.30 4.40 0.30 N 33 1 "O4'" B DC 24 ? ? "C1'" B DC 24 ? ? N1 B DC 24 ? ? 112.09 108.30 3.79 0.30 N 34 1 N3 B DC 24 ? ? C2 B DC 24 ? ? O2 B DC 24 ? ? 116.56 121.90 -5.35 0.70 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DA B 14 ? ? 0.076 'SIDE CHAIN' 2 1 DG B 19 ? ? 0.057 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LIA 'double helix' 2LIA 'b-form double helix' 2LIA '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 -0.431 -0.093 -0.492 -3.528 -14.166 3.037 1 A_DG1:DC24_B A 1 ? B 24 ? 19 1 1 A DA 2 1_555 B DT 11 1_555 -0.062 -0.019 0.168 11.015 -15.511 2.169 2 A_DA2:DT23_B A 2 ? B 23 ? 20 1 1 A DG 3 1_555 B DC 10 1_555 -0.239 -0.049 0.195 4.064 -4.877 -0.038 3 A_DG3:DC22_B A 3 ? B 22 ? 19 1 1 A DA 4 1_555 B DT 9 1_555 0.121 -0.022 -0.428 -3.849 -17.641 -2.624 4 A_DA4:DT21_B A 4 ? B 21 ? 20 1 1 A DC 6 1_555 B DG 7 1_555 0.376 -0.102 0.173 0.181 -7.648 -1.563 5 A_DC6:DG19_B A 6 ? B 19 ? 19 1 1 A DG 7 1_555 B DC 6 1_555 -0.418 -0.075 0.027 3.952 -5.877 0.145 6 A_DG7:DC18_B A 7 ? B 18 ? 19 1 1 A DT 9 1_555 B DA 4 1_555 -0.208 -0.072 -0.428 3.700 -19.708 -3.394 7 A_DT9:DA16_B A 9 ? B 16 ? 20 1 1 A DC 10 1_555 B DG 3 1_555 0.274 -0.122 0.045 -4.538 -8.527 -2.904 8 A_DC10:DG15_B A 10 ? B 15 ? 19 1 1 A DT 11 1_555 B DA 2 1_555 -0.037 -0.028 0.253 -6.931 -15.926 2.649 9 A_DT11:DA14_B A 11 ? B 14 ? 20 1 1 A DC 12 1_555 B DG 1 1_555 0.443 -0.088 -0.285 7.029 -17.999 0.561 10 A_DC12:DG13_B A 12 ? B 13 ? 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 12 1_555 A DA 2 1_555 B DT 11 1_555 0.021 -0.277 2.998 -5.937 -2.023 30.641 -0.162 -1.072 2.953 -3.778 11.089 31.261 1 AA_DG1DA2:DT23DC24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DA 2 1_555 B DT 11 1_555 A DG 3 1_555 B DC 10 1_555 -1.573 -0.531 3.305 -3.946 6.830 34.776 -1.883 1.984 3.298 11.249 6.499 35.632 2 AA_DA2DG3:DC22DT23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DG 3 1_555 B DC 10 1_555 A DA 4 1_555 B DT 9 1_555 -0.840 -0.091 3.560 2.009 11.970 33.683 -2.014 1.682 3.285 19.873 -3.335 35.743 3 AA_DG3DA4:DT21DC22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DA 4 1_555 B DT 9 1_555 A DC 6 1_555 B DG 7 1_555 0.200 -0.534 6.392 -3.757 5.550 69.049 -0.862 -0.441 6.322 4.885 3.306 69.333 4 AA_DA4DC6:DG19DT21_BB A 4 ? B 21 ? A 6 ? B 19 ? 1 A DC 6 1_555 B DG 7 1_555 A DG 7 1_555 B DC 6 1_555 0.063 -0.574 3.188 0.154 6.058 29.863 -2.251 -0.090 3.016 11.606 -0.294 30.458 5 AA_DC6DG7:DC18DG19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DG 7 1_555 B DC 6 1_555 A DT 9 1_555 B DA 4 1_555 -0.217 -0.736 6.543 3.230 6.303 69.631 -1.089 0.418 6.451 5.506 -2.821 69.945 6 AA_DG7DT9:DA16DC18_BB A 7 ? B 18 ? A 9 ? B 16 ? 1 A DT 9 1_555 B DA 4 1_555 A DC 10 1_555 B DG 3 1_555 0.772 -0.268 3.518 -0.883 12.156 36.833 -1.988 -1.279 3.253 18.623 1.353 38.730 7 AA_DT9DC10:DG15DA16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DC 10 1_555 B DG 3 1_555 A DT 11 1_555 B DA 2 1_555 0.950 -0.865 3.253 0.662 3.814 28.509 -2.580 -1.767 3.134 7.699 -1.337 28.765 8 AA_DC10DT11:DA14DG15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DT 11 1_555 B DA 2 1_555 A DC 12 1_555 B DG 1 1_555 -0.062 -0.383 3.050 4.815 -3.483 31.770 -0.110 0.911 3.032 -6.294 -8.701 32.307 9 AA_DT11DC12:DG13DA14_BB A 11 ? B 14 ? A 12 ? B 13 ? #