data_1BE5 # _entry.id 1BE5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.355 _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 1BE5 pdb_00001be5 10.2210/pdb1be5/pdb WWPDB D_1000171647 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1BE5 _pdbx_database_status.recvd_initial_deposition_date 1998-05-19 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.SG_entry ? _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 'Yang, X.-L.' 1 'Sugiyama, H.' 2 'Ikeda, S.' 3 'Saito, I.' 4 'Wang, A.H.-J.' 5 # _citation.id primary _citation.title ;Structural studies of a stable parallel-stranded DNA duplex incorporating isoguanine:cytosine and isocytosine:guanine basepairs by nuclear magnetic resonance spectroscopy. ; _citation.journal_abbrev Biophys.J. _citation.journal_volume 75 _citation.page_first 1163 _citation.page_last 1171 _citation.year 1998 _citation.journal_id_ASTM BIOJAU _citation.country US _citation.journal_id_ISSN 0006-3495 _citation.journal_id_CSD 0030 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9726918 _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yang, X.L.' 1 ? primary 'Sugiyama, H.' 2 ? primary 'Ikeda, S.' 3 ? primary 'Saito, I.' 4 ? primary 'Wang, A.H.' 5 ? # _cell.entry_id 1BE5 _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 1BE5 _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 DUPLEX (TGCACGGACT)' 3087.086 1 ? ? ? ? 2 polymer syn 'DNA DUPLEX (TGCACGGACT)' 3045.004 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 '(DT)(IGU)(IMC)(DA)(IMC)(IGU)(IGU)(DA)(IMC)(DT)' TGCACGGACT A ? 2 polydeoxyribonucleotide no no '(DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG)(DA)' ACGTGCCTGA B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DT n 1 2 IGU n 1 3 IMC n 1 4 DA n 1 5 IMC n 1 6 IGU n 1 7 IGU n 1 8 DA n 1 9 IMC n 1 10 DT n 2 1 DA n 2 2 DC n 2 3 DG n 2 4 DT n 2 5 DG n 2 6 DC n 2 7 DC n 2 8 DT n 2 9 DG n 2 10 DA n # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 1BE5 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession ? _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 1BE5 A 1 ? 10 ? 1BE5 1 ? 10 ? 1 10 2 1 1BE5 B 1 ? 10 ? 1BE5 11 ? 20 ? 11 20 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 IGU 'DNA linking' n "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 IMC 'DNA linking' n "N1-[2-DEOXY-RIBOFURANOSYL]-[2-AMINO-5-METHYL-4-OXO-4H-PYRIMIDINE]-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.solution_id 1 1 NOESY 1 2 1 TOCSY 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 275 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7.0 _pdbx_nmr_exptl_sample_conditions.ionic_strength '20mM PHOSPHATE BUFFER' _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents WATER # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength 1 'UNITY 750' Varian 750 2 'VXR 500' Varian 500 # _pdbx_nmr_refine.entry_id 1BE5 _pdbx_nmr_refine.method NOE-RMD _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_details.entry_id 1BE5 _pdbx_nmr_details.text 'THE STRUCTURE WAS DETERMINED USING 1H 2D NMR SPECTROSCOPY' # _pdbx_nmr_ensemble.entry_id 1BE5 _pdbx_nmr_ensemble.conformers_calculated_total_number 1 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'MINIMIZED AVERAGE' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR ? BRUNGER 1 'structure solution' X-PLOR ? ? 2 'structure solution' SPEDREF ? ? 3 # _exptl.entry_id 1BE5 _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 1BE5 _struct.title ;STRUCTURAL STUDIES OF A STABLE PARALLEL-STRANDED DNA DUPLEX INCORPORATING ISOGUANINE:CYTOSINE AND ISOCYTOSINE:GUANINE BASE PAIRS BY NMR, MINIMIZED AVERAGE STRUCTURE ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1BE5 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;DNA STRUCTURE, NOVEL DNA BASES, ANTISENSE OLIGONUCLEOTIDES, INTERCALATOR BINDING, REVERSE WATSON-CRICK BASE PAIRS, DEOXYRIBONUCLEIC ACID, 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 # 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 DT 1 "O3'" ? ? ? 1_555 A IGU 2 P ? ? A DT 1 A IGU 2 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale both ? A IGU 2 "O3'" ? ? ? 1_555 A IMC 3 P ? ? A IGU 2 A IMC 3 1_555 ? ? ? ? ? ? ? 1.634 ? ? covale3 covale both ? A IMC 3 "O3'" ? ? ? 1_555 A DA 4 P ? ? A IMC 3 A DA 4 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale4 covale both ? A DA 4 "O3'" ? ? ? 1_555 A IMC 5 P ? ? A DA 4 A IMC 5 1_555 ? ? ? ? ? ? ? 1.625 ? ? covale5 covale both ? A IMC 5 "O3'" ? ? ? 1_555 A IGU 6 P ? ? A IMC 5 A IGU 6 1_555 ? ? ? ? ? ? ? 1.622 ? ? covale6 covale both ? A IGU 6 "O3'" ? ? ? 1_555 A IGU 7 P ? ? A IGU 6 A IGU 7 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale7 covale both ? A IGU 7 "O3'" ? ? ? 1_555 A DA 8 P ? ? A IGU 7 A DA 8 1_555 ? ? ? ? ? ? ? 1.621 ? ? covale8 covale both ? A DA 8 "O3'" ? ? ? 1_555 A IMC 9 P ? ? A DA 8 A IMC 9 1_555 ? ? ? ? ? ? ? 1.632 ? ? covale9 covale both ? A IMC 9 "O3'" ? ? ? 1_555 A DT 10 P ? ? A IMC 9 A DT 10 1_555 ? ? ? ? ? ? ? 1.631 ? ? hydrog1 hydrog ? ? A IGU 2 N1 ? ? ? 1_555 B DC 2 O2 ? ? A IGU 2 B DC 12 1_555 ? ? ? ? ? ? 'IGU-DC PAIR' ? ? ? hydrog2 hydrog ? ? A IMC 3 N3 ? ? ? 1_555 B DG 3 N1 ? ? A IMC 3 B DG 13 1_555 ? ? ? ? ? ? 'IMC-DG PAIR' ? ? ? hydrog3 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 4 B DT 14 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog4 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 4 O2 ? ? A DA 4 B DT 14 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog5 hydrog ? ? A IMC 5 N3 ? ? ? 1_555 B DG 5 N1 ? ? A IMC 5 B DG 15 1_555 ? ? ? ? ? ? 'IMC-DG PAIR' ? ? ? hydrog6 hydrog ? ? A IGU 6 N1 ? ? ? 1_555 B DC 6 N3 ? ? A IGU 6 B DC 16 1_555 ? ? ? ? ? ? 'IGU-DC PAIR' ? ? ? hydrog7 hydrog ? ? A IGU 7 N1 ? ? ? 1_555 B DC 7 N3 ? ? A IGU 7 B DC 17 1_555 ? ? ? ? ? ? 'IGU-DC PAIR' ? ? ? hydrog8 hydrog ? ? A DA 8 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 8 B DT 18 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog9 hydrog ? ? A DA 8 N6 ? ? ? 1_555 B DT 8 O2 ? ? A DA 8 B DT 18 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog10 hydrog ? ? A IMC 9 N3 ? ? ? 1_555 B DG 9 N1 ? ? A IMC 9 B DG 19 1_555 ? ? ? ? ? ? 'IMC-DG PAIR' ? ? ? hydrog11 hydrog ? ? A DT 10 N3 ? ? ? 1_555 B DA 10 N1 ? ? A DT 10 B DA 20 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? hydrog12 hydrog ? ? A DT 10 O2 ? ? ? 1_555 B DA 10 N6 ? ? A DT 10 B DA 20 1_555 ? ? ? ? ? ? 'REVERSED WATSON-CRICK' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # _database_PDB_matrix.entry_id 1BE5 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 1BE5 _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 DT 1 1 1 DT T A . n A 1 2 IGU 2 2 2 IGU IGU A . n A 1 3 IMC 3 3 3 IMC IMC A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 IMC 5 5 5 IMC IMC A . n A 1 6 IGU 6 6 6 IGU IGU A . n A 1 7 IGU 7 7 7 IGU IGU A . n A 1 8 DA 8 8 8 DA A A . n A 1 9 IMC 9 9 9 IMC IMC A . n A 1 10 DT 10 10 10 DT T A . n B 2 1 DA 1 11 11 DA A B . n B 2 2 DC 2 12 12 DC C B . n B 2 3 DG 3 13 13 DG G B . n B 2 4 DT 4 14 14 DT T B . n B 2 5 DG 5 15 15 DG G B . n B 2 6 DC 6 16 16 DC C B . n B 2 7 DC 7 17 17 DC C B . n B 2 8 DT 8 18 18 DT T B . n B 2 9 DG 9 19 19 DG G B . n B 2 10 DA 10 20 20 DA A B . n # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A IGU 2 A IGU 2 ? DG "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" 2 A IMC 3 A IMC 3 ? DC ? 3 A IMC 5 A IMC 5 ? DC ? 4 A IGU 6 A IGU 6 ? DG "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" 5 A IGU 7 A IGU 7 ? DG "2'-DEOXYISOGUANINE-5'-MONOPHOSPHATE" 6 A IMC 9 A IMC 9 ? DC ? # _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 1998-08-12 2 'Structure model' 1 1 2008-03-24 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-02-16 # _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' 'Version format compliance' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' database_2 2 4 'Structure model' pdbx_database_status 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_oper_list 5 4 '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 4 'Structure model' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_database_status.process_site' 4 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 6 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 7 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 8 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 9 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 10 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 11 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 12 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 13 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 14 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' . ? 1 X-PLOR refinement . ? 2 X-PLOR phasing . ? 3 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C5'" A DT 1 ? ? "C4'" A DT 1 ? ? 1.581 1.512 0.069 0.007 N 2 1 C5 A DT 1 ? ? C7 A DT 1 ? ? 1.538 1.496 0.042 0.006 N 3 1 C5 A DT 10 ? ? C7 A DT 10 ? ? 1.538 1.496 0.042 0.006 N 4 1 "C3'" B DG 13 ? ? "C2'" B DG 13 ? ? 1.468 1.516 -0.048 0.008 N 5 1 "C5'" B DT 14 ? ? "C4'" B DT 14 ? ? 1.579 1.512 0.067 0.007 N 6 1 C5 B DT 14 ? ? C7 B DT 14 ? ? 1.535 1.496 0.039 0.006 N 7 1 "C5'" B DC 16 ? ? "C4'" B DC 16 ? ? 1.567 1.512 0.055 0.007 N # 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 DT 1 ? ? "C1'" A DT 1 ? ? N1 A DT 1 ? ? 112.36 108.30 4.06 0.30 N 2 1 N9 A DA 4 ? ? C4 A DA 4 ? ? C5 A DA 4 ? ? 108.22 105.80 2.42 0.40 N 3 1 "O4'" A DA 8 ? ? "C1'" A DA 8 ? ? N9 A DA 8 ? ? 111.38 108.30 3.08 0.30 N 4 1 "O4'" B DG 13 ? ? "C1'" B DG 13 ? ? N9 B DG 13 ? ? 114.97 108.30 6.67 0.30 N 5 1 "O4'" B DG 15 ? ? "C4'" B DG 15 ? ? "C3'" B DG 15 ? ? 111.34 106.00 5.34 0.60 N 6 1 "C4'" B DG 15 ? ? "C3'" B DG 15 ? ? "C2'" B DG 15 ? ? 96.94 102.20 -5.26 0.70 N 7 1 "O4'" B DC 17 ? ? "C1'" B DC 17 ? ? N1 B DC 17 ? ? 102.06 108.00 -5.94 0.70 N 8 1 "C4'" B DG 19 ? ? "C3'" B DG 19 ? ? "C2'" B DG 19 ? ? 96.33 102.20 -5.87 0.70 N 9 1 "O4'" B DG 19 ? ? "C1'" B DG 19 ? ? N9 B DG 19 ? ? 114.61 108.30 6.31 0.30 N 10 1 "O4'" B DA 20 ? ? "C1'" B DA 20 ? ? N9 B DA 20 ? ? 110.40 108.30 2.10 0.30 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 DT A 10 ? ? 0.098 'SIDE CHAIN' 2 1 DG B 15 ? ? 0.097 'SIDE CHAIN' 3 1 DA B 20 ? ? 0.085 'SIDE CHAIN' # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1BE5 'double helix' 1BE5 'parallel strands' # 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 IGU 2 1_555 B DC 2 1_555 0.150 1.544 -0.791 5.695 -10.430 162.979 1 A_IGU2:DC12_B A 2 ? B 12 ? ? 2 1 A IMC 3 1_555 B DG 3 1_555 -0.206 -1.625 0.141 -12.489 -9.332 -162.541 2 A_IMC3:DG13_B A 3 ? B 13 ? ? 2 1 A DA 4 1_555 B DT 4 1_555 0.269 1.880 -0.500 40.772 18.001 174.619 3 A_DA4:DT14_B A 4 ? B 14 ? 21 2 1 A IMC 5 1_555 B DG 5 1_555 -0.303 -1.976 0.056 -34.882 -2.744 -165.019 4 A_IMC5:DG15_B A 5 ? B 15 ? ? 2 1 A IGU 6 1_555 B DC 6 1_555 -0.052 0.714 -0.923 18.418 -24.195 172.349 5 A_IGU6:DC16_B A 6 ? B 16 ? ? ? 1 A IGU 7 1_555 B DC 7 1_555 0.092 1.041 -0.550 6.604 -19.865 168.266 6 A_IGU7:DC17_B A 7 ? B 17 ? ? ? 1 A DA 8 1_555 B DT 8 1_555 0.358 1.205 -0.307 19.942 1.029 177.551 7 A_DA8:DT18_B A 8 ? B 18 ? 21 2 1 A IMC 9 1_555 B DG 9 1_555 -0.214 -1.519 0.194 -23.730 1.728 -165.257 8 A_IMC9:DG19_B A 9 ? B 19 ? ? 2 1 A DT 10 1_555 B DA 10 1_555 -0.033 -1.685 1.054 -39.746 34.459 -164.305 9 A_DT10:DA20_B A 10 ? B 20 ? 21 2 # 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 IGU 2 1_555 B DC 2 1_555 A IMC 3 1_555 B DG 3 1_555 -2.120 -0.385 2.561 7.065 -6.811 -156.520 0.213 -1.066 2.583 3.478 3.608 -156.607 1 AA_IGU2IMC3:DG13DC12_BB A 2 ? B 12 ? A 3 ? B 13 ? 1 A IMC 3 1_555 B DG 3 1_555 A DA 4 1_555 B DT 4 1_555 -1.031 1.161 3.024 6.161 4.231 -136.600 -0.649 -0.520 3.028 -2.277 3.315 -136.697 2 AA_IMC3DA4:DT14DG13_BB A 3 ? B 13 ? A 4 ? B 14 ? 1 A DA 4 1_555 B DT 4 1_555 A IMC 5 1_555 B DG 5 1_555 -0.876 0.528 3.464 5.513 3.736 -137.300 -0.307 -0.435 3.472 -2.005 2.959 -137.376 3 AA_DA4IMC5:DG15DT14_BB A 4 ? B 14 ? A 5 ? B 15 ? 1 A IMC 5 1_555 B DG 5 1_555 A IGU 6 1_555 B DC 6 1_555 -0.407 1.030 3.450 10.606 8.730 -141.348 -0.594 -0.156 3.433 -4.623 5.617 -141.637 4 AA_IMC5IGU6:DC16DG15_BB A 5 ? B 15 ? A 6 ? B 16 ? 1 A IGU 6 1_555 B DC 6 1_555 A IGU 7 1_555 B DC 7 1_555 0.173 0.304 2.884 -5.919 -1.462 37.511 0.631 -0.927 2.812 -2.255 9.130 37.986 5 AA_IGU6IGU7:DC17DC16_BB A 6 ? B 16 ? A 7 ? B 17 ? 1 A IGU 7 1_555 B DC 7 1_555 A DA 8 1_555 B DT 8 1_555 -0.585 0.705 2.764 -4.025 1.310 30.249 1.115 0.422 2.844 2.494 7.666 30.537 6 AA_IGU7DA8:DT18DC17_BB A 7 ? B 17 ? A 8 ? B 18 ? 1 A DA 8 1_555 B DT 8 1_555 A IMC 9 1_555 B DG 9 1_555 -0.708 0.560 3.330 7.124 2.405 -146.173 -0.304 -0.337 3.339 -1.256 3.723 -146.248 7 AA_DA8IMC9:DG19DT18_BB A 8 ? B 18 ? A 9 ? B 19 ? 1 A IMC 9 1_555 B DG 9 1_555 A DT 10 1_555 B DA 10 1_555 0.815 0.056 4.076 -7.347 -0.547 52.435 0.106 -1.497 3.936 -0.615 8.268 52.914 8 AA_IMC9DT10:DA20DG19_BB A 9 ? B 19 ? A 10 ? B 20 ? #