data_3REC # _entry.id 3REC # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.356 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3REC pdb_00003rec 10.2210/pdb3rec/pdb WWPDB D_1000179129 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1EW1 _pdbx_database_related.details 'ENSEMBLE OF 10 STRUCTURES' _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3REC _pdbx_database_status.recvd_initial_deposition_date 1997-04-17 _pdbx_database_status.deposit_site ? _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf ? _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 'Nishinaka, T.' 1 'Ito, Y.' 2 'Yokoyama, S.' 3 'Shibata, T.' 4 # _citation.id primary _citation.title 'An extended DNA structure through deoxyribose-base stacking induced by RecA protein.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 94 _citation.page_first 6623 _citation.page_last 6628 _citation.year 1997 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 9192615 _citation.pdbx_database_id_DOI 10.1073/pnas.94.13.6623 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nishinaka, T.' 1 ? primary 'Ito, Y.' 2 ? primary 'Yokoyama, S.' 3 ? primary 'Shibata, T.' 4 ? # _cell.entry_id 3REC _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 3REC _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*TP*A)-3') ; _entity.formula_weight 572.442 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details 'D(TA) REGION OF D(TACG) RECA PROTEIN-BOUND DNA' # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DT)(DA)' _entity_poly.pdbx_seq_one_letter_code_can TA _entity_poly.pdbx_strand_id A _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 DT n 1 2 DA n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 3REC _struct_ref.pdbx_db_accession 3REC _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3REC _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 2 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 3REC _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 2 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 2 # 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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 # _pdbx_nmr_exptl.experiment_id 1 _pdbx_nmr_exptl.conditions_id 1 _pdbx_nmr_exptl.type 'TRANSFERRED NOESY' _pdbx_nmr_exptl.solution_id 1 # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 303 _pdbx_nmr_exptl_sample_conditions.pressure ? _pdbx_nmr_exptl_sample_conditions.pH 7.1 _pdbx_nmr_exptl_sample_conditions.ionic_strength ? _pdbx_nmr_exptl_sample_conditions.pressure_units . _pdbx_nmr_exptl_sample_conditions.temperature_units K # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AMX600 _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 # _pdbx_nmr_refine.entry_id 3REC _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details 'REFINEMENT DETAILS CAN BE FOUND IN THE MATERIAL AND METHODS SECTION OF THE ABOVE REFERENCE.' _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 3REC _pdbx_nmr_ensemble.conformers_calculated_total_number 100 _pdbx_nmr_ensemble.conformers_submitted_total_number 1 _pdbx_nmr_ensemble.conformer_selection_criteria 'LEAST OVERALL ENERGY' # loop_ _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors _pdbx_nmr_software.ordinal refinement X-PLOR 3.1 BRUNGER 1 'structure solution' X-PLOR ? ? 2 # _exptl.entry_id 3REC _exptl.method 'SOLUTION NMR' _exptl.crystals_number ? # _struct.entry_id 3REC _struct.title 'ESCHERICHIA COLI RECA PROTEIN-BOUND DNA, NMR, 1 STRUCTURE' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3REC _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'DEOXYRIBOSE-BASE STACKING, HOMOLOGOUS RECOMBINATION, HOMOLOGOUS PAIRING, DEOXYRIBONUCLEIC ACID, DNA' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_biol.id 1 # _database_PDB_matrix.entry_id 3REC _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 3REC _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_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 O "O5'" . DT A 1 1 ? 6.823 -2.711 6.110 1.00 0.00 ? 1 DT A "O5'" 1 ATOM 2 C "C5'" . DT A 1 1 ? 7.938 -1.871 6.464 1.00 0.00 ? 1 DT A "C5'" 1 ATOM 3 C "C4'" . DT A 1 1 ? 7.452 -0.639 7.195 1.00 0.00 ? 1 DT A "C4'" 1 ATOM 4 O "O4'" . DT A 1 1 ? 6.144 -0.280 6.693 1.00 0.00 ? 1 DT A "O4'" 1 ATOM 5 C "C3'" . DT A 1 1 ? 7.285 -0.842 8.701 1.00 0.00 ? 1 DT A "C3'" 1 ATOM 6 O "O3'" . DT A 1 1 ? 7.586 0.381 9.390 1.00 0.00 ? 1 DT A "O3'" 1 ATOM 7 C "C2'" . DT A 1 1 ? 5.808 -1.150 8.845 1.00 0.00 ? 1 DT A "C2'" 1 ATOM 8 C "C1'" . DT A 1 1 ? 5.190 -0.306 7.745 1.00 0.00 ? 1 DT A "C1'" 1 ATOM 9 N N1 . DT A 1 1 ? 3.932 -0.849 7.204 1.00 0.00 ? 1 DT A N1 1 ATOM 10 C C2 . DT A 1 1 ? 2.869 0.009 7.039 1.00 0.00 ? 1 DT A C2 1 ATOM 11 O O2 . DT A 1 1 ? 2.921 1.195 7.319 1.00 0.00 ? 1 DT A O2 1 ATOM 12 N N3 . DT A 1 1 ? 1.736 -0.576 6.530 1.00 0.00 ? 1 DT A N3 1 ATOM 13 C C4 . DT A 1 1 ? 1.566 -1.902 6.178 1.00 0.00 ? 1 DT A C4 1 ATOM 14 O O4 . DT A 1 1 ? 0.487 -2.283 5.733 1.00 0.00 ? 1 DT A O4 1 ATOM 15 C C5 . DT A 1 1 ? 2.722 -2.745 6.378 1.00 0.00 ? 1 DT A C5 1 ATOM 16 C C7 . DT A 1 1 ? 2.633 -4.196 6.026 1.00 0.00 ? 1 DT A C7 1 ATOM 17 C C6 . DT A 1 1 ? 3.832 -2.184 6.874 1.00 0.00 ? 1 DT A C6 1 ATOM 18 H "H5'" . DT A 1 1 ? 8.463 -1.568 5.558 1.00 0.00 ? 1 DT A "H5'" 1 ATOM 19 H "H5''" . DT A 1 1 ? 8.618 -2.428 7.109 1.00 0.00 ? 1 DT A "H5''" 1 ATOM 20 H "H4'" . DT A 1 1 ? 8.147 0.184 7.027 1.00 0.00 ? 1 DT A "H4'" 1 ATOM 21 H "H3'" . DT A 1 1 ? 7.894 -1.674 9.053 1.00 0.00 ? 1 DT A "H3'" 1 ATOM 22 H "H2'" . DT A 1 1 ? 5.610 -2.209 8.687 1.00 0.00 ? 1 DT A "H2'" 1 ATOM 23 H "H2''" . DT A 1 1 ? 5.438 -0.852 9.825 1.00 0.00 ? 1 DT A "H2''" 1 ATOM 24 H "H1'" . DT A 1 1 ? 5.026 0.704 8.121 1.00 0.00 ? 1 DT A "H1'" 1 ATOM 25 H H3 . DT A 1 1 ? 0.938 0.029 6.398 1.00 0.00 ? 1 DT A H3 1 ATOM 26 H H71 . DT A 1 1 ? 2.823 -4.798 6.915 1.00 0.00 ? 1 DT A H71 1 ATOM 27 H H72 . DT A 1 1 ? 3.375 -4.431 5.263 1.00 0.00 ? 1 DT A H72 1 ATOM 28 H H73 . DT A 1 1 ? 1.636 -4.417 5.644 1.00 0.00 ? 1 DT A H73 1 ATOM 29 H H6 . DT A 1 1 ? 4.705 -2.818 7.025 1.00 0.00 ? 1 DT A H6 1 ATOM 30 H "HO5'" . DT A 1 1 ? 6.384 -2.961 6.926 1.00 0.00 ? 1 DT A "HO5'" 1 ATOM 31 P P . DA A 1 2 ? 8.546 0.352 10.679 1.00 0.00 ? 2 DA A P 1 ATOM 32 O OP1 . DA A 1 2 ? 9.828 0.994 10.293 1.00 0.00 ? 2 DA A OP1 1 ATOM 33 O OP2 . DA A 1 2 ? 8.551 -1.028 11.226 1.00 0.00 ? 2 DA A OP2 1 ATOM 34 O "O5'" . DA A 1 2 ? 7.812 1.303 11.726 1.00 0.00 ? 2 DA A "O5'" 1 ATOM 35 C "C5'" . DA A 1 2 ? 7.627 2.704 11.451 1.00 0.00 ? 2 DA A "C5'" 1 ATOM 36 C "C4'" . DA A 1 2 ? 6.387 3.214 12.150 1.00 0.00 ? 2 DA A "C4'" 1 ATOM 37 O "O4'" . DA A 1 2 ? 5.272 2.358 11.811 1.00 0.00 ? 2 DA A "O4'" 1 ATOM 38 C "C3'" . DA A 1 2 ? 6.487 3.192 13.675 1.00 0.00 ? 2 DA A "C3'" 1 ATOM 39 O "O3'" . DA A 1 2 ? 5.773 4.296 14.240 1.00 0.00 ? 2 DA A "O3'" 1 ATOM 40 C "C2'" . DA A 1 2 ? 5.817 1.883 14.043 1.00 0.00 ? 2 DA A "C2'" 1 ATOM 41 C "C1'" . DA A 1 2 ? 4.738 1.759 12.983 1.00 0.00 ? 2 DA A "C1'" 1 ATOM 42 N N9 . DA A 1 2 ? 4.374 0.381 12.658 1.00 0.00 ? 2 DA A N9 1 ATOM 43 C C8 . DA A 1 2 ? 5.194 -0.720 12.626 1.00 0.00 ? 2 DA A C8 1 ATOM 44 N N7 . DA A 1 2 ? 4.577 -1.829 12.299 1.00 0.00 ? 2 DA A N7 1 ATOM 45 C C5 . DA A 1 2 ? 3.261 -1.433 12.101 1.00 0.00 ? 2 DA A C5 1 ATOM 46 C C6 . DA A 1 2 ? 2.116 -2.133 11.683 1.00 0.00 ? 2 DA A C6 1 ATOM 47 N N6 . DA A 1 2 ? 2.098 -3.444 11.435 1.00 0.00 ? 2 DA A N6 1 ATOM 48 N N1 . DA A 1 2 ? 0.973 -1.430 11.528 1.00 0.00 ? 2 DA A N1 1 ATOM 49 C C2 . DA A 1 2 ? 0.991 -0.115 11.777 1.00 0.00 ? 2 DA A C2 1 ATOM 50 N N3 . DA A 1 2 ? 2.002 0.654 12.174 1.00 0.00 ? 2 DA A N3 1 ATOM 51 C C4 . DA A 1 2 ? 3.122 -0.074 12.319 1.00 0.00 ? 2 DA A C4 1 ATOM 52 H "H5'" . DA A 1 2 ? 7.520 2.849 10.376 1.00 0.00 ? 2 DA A "H5'" 1 ATOM 53 H "H5''" . DA A 1 2 ? 8.495 3.259 11.807 1.00 0.00 ? 2 DA A "H5''" 1 ATOM 54 H "H4'" . DA A 1 2 ? 6.177 4.233 11.826 1.00 0.00 ? 2 DA A "H4'" 1 ATOM 55 H "H3'" . DA A 1 2 ? 7.527 3.203 13.999 1.00 0.00 ? 2 DA A "H3'" 1 ATOM 56 H "HO3'" . DA A 1 2 ? 4.846 4.178 14.022 1.00 0.00 ? 2 DA A "HO3'" 1 ATOM 57 H "H2'" . DA A 1 2 ? 6.520 1.052 13.988 1.00 0.00 ? 2 DA A "H2'" 1 ATOM 58 H "H2''" . DA A 1 2 ? 5.384 1.930 15.042 1.00 0.00 ? 2 DA A "H2''" 1 ATOM 59 H "H1'" . DA A 1 2 ? 3.855 2.308 13.310 1.00 0.00 ? 2 DA A "H1'" 1 ATOM 60 H H8 . DA A 1 2 ? 6.258 -0.676 12.851 1.00 0.00 ? 2 DA A H8 1 ATOM 61 H H61 . DA A 1 2 ? 1.243 -3.890 11.135 1.00 0.00 ? 2 DA A H61 1 ATOM 62 H H62 . DA A 1 2 ? 2.940 -3.991 11.547 1.00 0.00 ? 2 DA A H62 1 ATOM 63 H H2 . DA A 1 2 ? 0.044 0.398 11.635 1.00 0.00 ? 2 DA A H2 1 # 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 DA 2 2 2 DA A A . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # _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 1997-10-22 2 'Structure model' 1 1 2008-03-25 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2022-03-16 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' '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 # 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' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal X-PLOR 'model building' 3.1 ? 1 X-PLOR refinement 3.1 ? 2 X-PLOR phasing 3.1 ? 3 #