data_2LB4 # _entry.id 2LB4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2LB4 RCSB RCSB102180 WWPDB D_1000102180 # loop_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 2LAR PDB 'DNA / RNA hybrid containing other stereo specific borano modification' unspecified 17535 BMRB 'DNA / RNA hybrid containing other stereo specific borano modification' # _pdbx_database_status.deposit_site BMRB _pdbx_database_status.entry_id 2LB4 _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2011-03-22 _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.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Johnson, C.N.' 1 'Spring, A.M.' 2 'Shaw, B.R.' 3 'Germann, M.W.' 4 # _citation.id primary _citation.title 'Structural Basis of the RNase H1 Activity on Stereo Regular Borano Phosphonate DNA/RNA Hybrids.' _citation.journal_abbrev Biochemistry _citation.journal_volume 50 _citation.page_first 3903 _citation.page_last 3912 _citation.year 2011 _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 21443203 _citation.pdbx_database_id_DOI 10.1021/bi200083d # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Johnson, C.N.' 1 primary 'Spring, A.M.' 2 primary 'Sergueev, D.' 3 primary 'Shaw, B.R.' 4 primary 'Germann, M.W.' 5 # _cell.entry_id 2LB4 _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 2LB4 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn "DNA_(5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')_" 2743.637 1 ? ? ? ? 2 polymer syn "RNA_(5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')_" 2854.782 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 '(DA)(DT)(DG)(DG)(DT)(BGR)(DC)(DT)(DC)' ATGGTXCTC A ? 2 polyribonucleotide no no GAGCACCAU GAGCACCAU B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DA n 1 2 DT n 1 3 DG n 1 4 DG n 1 5 DT n 1 6 BGR n 1 7 DC n 1 8 DT n 1 9 DC n 2 1 G n 2 2 A n 2 3 G n 2 4 C n 2 5 A n 2 6 C n 2 7 C n 2 8 A n 2 9 U 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 2LB4 2LB4 1 ? ? ? 2 PDB 2LB4 2LB4 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 2LB4 A 1 ? 9 ? 2LB4 1 ? 9 ? 1 9 2 2 2LB4 B 1 ? 9 ? 2LB4 10 ? 18 ? 10 18 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y "ADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 BGR non-polymer . '[[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]boranuide' ? 'C10 H16 B N5 O6 P -1' 344.049 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 U 'RNA linking' y "URIDINE-5'-MONOPHOSPHATE" ? 'C9 H13 N2 O9 P' 324.181 # 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 2 '2D 1H-13C HSQC' 1 3 2 '2D 1H-1H TOCSY' 1 4 2 '2D 1H-1H NOESY' 1 5 2 '2D DQF-COSY' 1 6 2 '2D 1H-31P CORR' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.ionic_strength 50 _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 # loop_ _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.solvent_system ;1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS, 10 % D2O, 90 % H2O, 90% H2O/10% D2O ; 1 '90% H2O/10% D2O' ;1.0 mM DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3'), 1.0 mM RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3'), 50 mM sodium chloride, 10 mM sodium phosphate, 0.5 mM EDTA, 0.3 uM DSS, 99.999 % D2O ; 2 '99.999 % D2O' # loop_ _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.type 600 Bruker Avance 1 'Bruker Avance' 500 Bruker Avance 2 'Bruker Avance' # _pdbx_nmr_refine.entry_id 2LB4 _pdbx_nmr_refine.method 'molecular 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 'structure with lowest restraint violations' _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 2LB4 _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 2LB4 _pdbx_nmr_representative.selection_criteria 'structure with lowest restraint violations' # loop_ _pdbx_nmr_software.authors _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.ordinal 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' 'structure solution' AMBER 9.0 1 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' 'geometry optimization' AMBER 9.0 2 'Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm' refinement AMBER 9.0 3 'Bruker Biospin' collection XWINNMR 3.5 4 'Bruker Biospin' 'data analysis' TOPSPIN 2.1 5 'Bruker Biospin' processing TOPSPIN 2.1 6 'Thomas James' 'data analysis' CORMA 5.21 7 'Thomas James' refinement MARDIGRAS 5.21 8 Goddard 'data analysis' SPARKY 3.98 9 Goddard 'chemical shift assignment' SPARKY 3.98 10 # _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 2LB4 _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 2LB4 _struct.title 'DNA / RNA Hybrid containing a central stereo specific Sp borano phosphate linkage' _struct.pdbx_descriptor "5'-D(*AP*TP*GP*GP*TP*(BGR)P*CP*TP*C)-3'" _struct.pdbx_model_details 'structure with lowest restraint violations, model 1' _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2LB4 _struct_keywords.pdbx_keywords DNA/RNA _struct_keywords.text 'nucleic acid heteroduplex, RNase H1 activity, DNA-RNA complex' # 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 covale1 covale ? ? A DT 5 "O3'" ? ? ? 1_555 A BGR 6 P ? ? A DT 5 A BGR 6 1_555 ? ? ? ? ? ? ? 1.626 ? hydrog1 hydrog ? ? A DA 1 N1 ? ? ? 1_555 B U 9 N3 ? ? A DA 1 B U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog2 hydrog ? ? A DA 1 N6 ? ? ? 1_555 B U 9 O4 ? ? A DA 1 B U 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog3 hydrog ? ? A DT 2 N3 ? ? ? 1_555 B A 8 N1 ? ? A DT 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog4 hydrog ? ? A DT 2 O4 ? ? ? 1_555 B A 8 N6 ? ? A DT 2 B A 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog5 hydrog ? ? A DG 3 N1 ? ? ? 1_555 B C 7 N3 ? ? A DG 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog6 hydrog ? ? A DG 3 N2 ? ? ? 1_555 B C 7 O2 ? ? A DG 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog7 hydrog ? ? A DG 3 O6 ? ? ? 1_555 B C 7 N4 ? ? A DG 3 B C 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog8 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B C 6 N3 ? ? A DG 4 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog9 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B C 6 O2 ? ? A DG 4 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog10 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B C 6 N4 ? ? A DG 4 B C 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog11 hydrog ? ? A DT 5 N3 ? ? ? 1_555 B A 5 N1 ? ? A DT 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog12 hydrog ? ? A DT 5 O4 ? ? ? 1_555 B A 5 N6 ? ? A DT 5 B A 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog13 hydrog ? ? A DC 7 N3 ? ? ? 1_555 B G 3 N1 ? ? A DC 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog14 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B G 3 O6 ? ? A DC 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog15 hydrog ? ? A DC 7 O2 ? ? ? 1_555 B G 3 N2 ? ? A DC 7 B G 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog16 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B A 2 N1 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog17 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B A 2 N6 ? ? A DT 8 B A 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog18 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog19 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? hydrog20 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 9 B G 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _atom_sites.entry_id 2LB4 _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 B 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 DA 1 1 1 DA DA 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 DT 5 5 5 DT DT A . n A 1 6 BGR 6 6 6 BGR BGS 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 DC 9 9 9 DC DC A . n B 2 1 G 1 10 10 G G B . n B 2 2 A 2 11 11 A A B . n B 2 3 G 3 12 12 G G B . n B 2 4 C 4 13 13 C C B . n B 2 5 A 5 14 14 A A B . n B 2 6 C 6 15 15 C C B . n B 2 7 C 7 16 16 C C B . n B 2 8 A 8 17 17 A A B . n B 2 9 U 9 18 18 U U 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 2011-06-29 2 'Structure model' 1 1 2011-07-13 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # 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(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')-1 ; 1.0 ? mM ? 1 ;RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')-2 ; 1.0 ? mM ? 1 'sodium chloride-3' 50 ? mM ? 1 'sodium phosphate-4' 10 ? mM ? 1 EDTA-5 0.5 ? mM ? 1 DSS-6 0.3 ? uM ? 1 D2O-7 10 ? % ? 1 H2O-8 90 ? % ? 1 ;DNA (5'-D(*AP*TP*GP*GP*TP*BGR*CP*TP*C)-3')-9 ; 1.0 ? mM ? 2 ;RNA (5'-R(*GP*AP*GP*CP*AP*CP*CP*AP*U)-3')-10 ; 1.0 ? mM ? 2 'sodium chloride-11' 50 ? mM ? 2 'sodium phosphate-12' 10 ? mM ? 2 EDTA-13 0.5 ? mM ? 2 DSS-14 0.3 ? uM ? 2 D2O-15 99.999 ? % ? 2 # 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 DA 1 ? ? "C4'" A DA 1 ? ? "C3'" A DA 1 ? ? 110.23 106.00 4.23 0.60 N 2 1 "O4'" A DA 1 ? ? "C1'" A DA 1 ? ? N9 A DA 1 ? ? 112.04 108.30 3.74 0.30 N 3 1 C4 A DA 1 ? ? C5 A DA 1 ? ? C6 A DA 1 ? ? 113.20 117.00 -3.80 0.50 N 4 1 C5 A DA 1 ? ? C6 A DA 1 ? ? N1 A DA 1 ? ? 120.85 117.70 3.15 0.50 N 5 1 N1 A DA 1 ? ? C6 A DA 1 ? ? N6 A DA 1 ? ? 112.07 118.60 -6.53 0.60 N 6 1 "O4'" A DT 2 ? ? "C1'" A DT 2 ? ? N1 A DT 2 ? ? 110.42 108.30 2.12 0.30 N 7 1 C6 A DT 2 ? ? C5 A DT 2 ? ? C7 A DT 2 ? ? 119.30 122.90 -3.60 0.60 N 8 1 "C4'" A DT 5 ? ? "C3'" A DT 5 ? ? "C2'" A DT 5 ? ? 97.45 102.20 -4.75 0.70 N 9 1 "O4'" A DT 5 ? ? "C1'" A DT 5 ? ? N1 A DT 5 ? ? 112.28 108.30 3.98 0.30 N 10 1 C6 A DT 5 ? ? C5 A DT 5 ? ? C7 A DT 5 ? ? 119.29 122.90 -3.61 0.60 N 11 1 "C3'" A DC 7 ? ? "C2'" A DC 7 ? ? "C1'" A DC 7 ? ? 110.01 102.50 7.51 1.20 N 12 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 111.79 108.30 3.49 0.30 N 13 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? N1 A DT 8 ? ? 110.46 108.30 2.16 0.30 N 14 1 C6 A DT 8 ? ? C5 A DT 8 ? ? C7 A DT 8 ? ? 118.84 122.90 -4.06 0.60 N 15 1 "O4'" A DC 9 ? ? "C1'" A DC 9 ? ? N1 A DC 9 ? ? 110.36 108.30 2.06 0.30 N 16 1 N3 A DC 9 ? ? C2 A DC 9 ? ? O2 A DC 9 ? ? 117.61 121.90 -4.29 0.70 N 17 1 "C3'" B G 10 ? ? "C2'" B G 10 ? ? "C1'" B G 10 ? ? 106.35 101.50 4.85 0.80 N 18 1 C5 B A 11 ? ? C6 B A 11 ? ? N1 B A 11 ? ? 122.08 117.70 4.38 0.50 N 19 1 C5 B A 14 ? ? C6 B A 14 ? ? N1 B A 14 ? ? 120.72 117.70 3.02 0.50 N 20 1 N1 B A 14 ? ? C6 B A 14 ? ? N6 B A 14 ? ? 113.97 118.60 -4.63 0.60 N 21 1 "C5'" B C 15 ? ? "C4'" B C 15 ? ? "O4'" B C 15 ? ? 116.29 109.80 6.49 0.90 N 22 1 N3 B C 16 ? ? C2 B C 16 ? ? O2 B C 16 ? ? 117.40 121.90 -4.50 0.70 N 23 1 C4 B A 17 ? ? C5 B A 17 ? ? C6 B A 17 ? ? 112.47 117.00 -4.53 0.50 N 24 1 C6 B A 17 ? ? C5 B A 17 ? ? N7 B A 17 ? ? 136.79 132.30 4.49 0.70 N 25 1 N1 B A 17 ? ? C6 B A 17 ? ? N6 B A 17 ? ? 111.61 118.60 -6.99 0.60 N 26 1 "O4'" B U 18 ? ? "C1'" B U 18 ? ? N1 B U 18 ? ? 114.09 108.50 5.59 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 DG A 3 ? ? 0.073 'SIDE CHAIN' 2 1 DG A 4 ? ? 0.065 'SIDE CHAIN' 3 1 A B 17 ? ? 0.067 'SIDE CHAIN' 4 1 U B 18 ? ? 0.084 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 2LB4 'double helix' 2LB4 'a-form double helix' 2LB4 '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 DA 1 1_555 B U 9 1_555 0.214 0.044 -0.104 -11.804 11.249 6.023 1 A_DA1:U18_B A 1 ? B 18 ? 20 1 1 A DT 2 1_555 B A 8 1_555 -0.455 -0.056 -0.285 11.819 1.177 11.450 2 A_DT2:A17_B A 2 ? B 17 ? 20 1 1 A DG 3 1_555 B C 7 1_555 -0.198 -0.122 -0.249 -0.888 -14.124 -0.756 3 A_DG3:C16_B A 3 ? B 16 ? 19 1 1 A DG 4 1_555 B C 6 1_555 -0.013 -0.024 -0.275 -14.662 -10.632 1.634 4 A_DG4:C15_B A 4 ? B 15 ? 19 1 1 A DT 5 1_555 B A 5 1_555 -0.055 0.036 0.264 -9.947 -11.405 5.712 5 A_DT5:A14_B A 5 ? B 14 ? 20 1 1 A DC 7 1_555 B G 3 1_555 0.089 -0.082 -0.103 13.500 -11.724 -4.726 6 A_DC7:G12_B A 7 ? B 12 ? 19 1 1 A DT 8 1_555 B A 2 1_555 -0.284 0.068 -0.179 13.314 -15.941 -10.109 7 A_DT8:A11_B A 8 ? B 11 ? 20 1 1 A DC 9 1_555 B G 1 1_555 -0.064 -0.021 0.162 2.555 -27.457 1.081 8 A_DC9:G10_B A 9 ? B 10 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DA 1 1_555 B U 9 1_555 A DT 2 1_555 B A 8 1_555 0.070 -2.064 2.957 1.984 5.882 22.040 -6.925 0.404 2.331 15.007 -5.061 22.887 1 AA_DA1DT2:A17U18_BB A 1 ? B 18 ? A 2 ? B 17 ? 1 A DT 2 1_555 B A 8 1_555 A DG 3 1_555 B C 7 1_555 -2.089 -0.683 3.553 -4.772 4.597 38.328 -1.648 2.493 3.674 6.938 7.202 38.875 2 AA_DT2DG3:C16A17_BB A 2 ? B 17 ? A 3 ? B 16 ? 1 A DG 3 1_555 B C 7 1_555 A DG 4 1_555 B C 6 1_555 -0.353 -1.466 3.554 -0.880 9.318 35.326 -3.671 0.438 3.089 15.031 1.419 36.506 3 AA_DG3DG4:C15C16_BB A 3 ? B 16 ? A 4 ? B 15 ? 1 A DG 4 1_555 B C 6 1_555 A DT 5 1_555 B A 5 1_555 0.698 -0.996 3.105 -3.356 7.097 27.593 -3.454 -2.091 2.669 14.511 6.863 28.667 4 AA_DG4DT5:A14C15_BB A 4 ? B 15 ? A 5 ? B 14 ? 1 A DT 5 1_555 B A 5 1_555 A DC 7 1_555 B G 3 1_555 -0.217 -2.658 5.903 4.470 12.388 60.153 -3.612 0.577 5.291 12.201 -4.402 61.446 5 AA_DT5DC7:G12A14_BB A 5 ? B 14 ? A 7 ? B 12 ? 1 A DC 7 1_555 B G 3 1_555 A DT 8 1_555 B A 2 1_555 -0.433 -1.442 3.367 1.382 4.802 30.681 -3.606 1.071 3.089 9.000 -2.590 31.076 6 AA_DC7DT8:A11G12_BB A 7 ? B 12 ? A 8 ? B 11 ? 1 A DT 8 1_555 B A 2 1_555 A DC 9 1_555 B G 1 1_555 0.910 -0.761 3.402 1.906 6.000 39.064 -1.850 -1.115 3.294 8.903 -2.828 39.548 7 AA_DT8DC9:G10A11_BB A 8 ? B 11 ? A 9 ? B 10 ? #