data_1D62 # _entry.id 1D62 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.374 _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 1D62 pdb_00001d62 10.2210/pdb1d62/pdb RCSB BD0055 ? ? WWPDB D_1000172663 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D62 _pdbx_database_status.recvd_initial_deposition_date 1992-03-01 _pdbx_database_status.deposit_site NDB _pdbx_database_status.process_site NDB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _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 'Lipanov, A.' 1 'Kopka, M.L.' 2 'Kaczor-Grzeskowiak, M.' 3 'Dickerson, R.E.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Structure of the B-DNA decamer C-C-A-A-C-I-T-T-G-G in two different space groups: conformational flexibility of B-DNA.' Biochemistry 32 1373 1389 1993 BICHAW US 0006-2960 0033 ? 8448146 10.1021/bi00056a024 1 ;The Structure of the /B-DNA Decamer / C-C-A-A-C-G-T-T-G-G and Comparison with the Isomorphous Decamers /C-C-A-A-G-A-T-T-G-G and /C-C-A-G-G-C-C-T-G-G ; J.Mol.Biol. 217 177 199 1991 JMOBAK UK 0022-2836 0070 ? ? ? 2 'Crystallographic Study of One Turn of G(Slash)C-Rich B-/DNA' J.Mol.Biol. 210 369 381 1989 JMOBAK UK 0022-2836 0070 ? ? ? 3 'Helix Geometry, Hydration, and G(Dot)A Mismatch in a B-/DNA Decamer' Science 238 498 504 1987 SCIEAS US 0036-8075 0038 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lipanov, A.A.' 1 ? primary 'Kopka, M.L.' 2 ? primary 'Kaczor-Grzeskowiak, M.' 3 ? primary 'Dickerson, R.E.' 4 ? 1 'Prive, G.G.' 5 ? 1 'Yanagi, K.' 6 ? 1 'Dickerson, R.E.' 7 ? 2 'Heinemann, U.' 8 ? 2 'Alings, C.' 9 ? 3 'Prive, G.G.' 10 ? 3 'Heinemann, U.' 11 ? 3 'Chandrasegaran, S.' 12 ? 3 'Kan, L.-S.' 13 ? 3 'Kopka, M.L.' 14 ? 3 'Dickerson, R.E.' 15 ? # _cell.entry_id 1D62 _cell.length_a 32.210 _cell.length_b 25.140 _cell.length_c 34.140 _cell.angle_alpha 90.00 _cell.angle_beta 114.70 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D62 _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # 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 "5'-D(*CP*CP*AP*AP*IP*AP*TP*TP*GP*G)-3'" 3054.016 1 ? ? ? ? 2 water nat water 18.015 50 ? ? ? ? # _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 '(DC)(DC)(DA)(DA)(DI)(DA)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAAIATTGG _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 DC n 1 2 DC n 1 3 DA n 1 4 DA n 1 5 DI n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DG n 1 10 DG n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1D62 _struct_ref.pdbx_db_accession 1D62 _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 1D62 _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 10 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1D62 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 10 _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 10 # 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 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 1D62 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.97 _exptl_crystal.density_percent_sol 37.67 _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine.entry_id 1D62 _refine.ls_number_reflns_obs 1195 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.0 _refine.ls_d_res_high 2.0 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1340000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 203 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 50 _refine_hist.number_atoms_total 253 _refine_hist.d_res_high 2.0 _refine_hist.d_res_low 8.0 # _struct.entry_id 1D62 _struct.title 'THE STRUCTURE OF A /B-DNA$ DECAMER WITH AN I(SLASH)*A MISMATCH AND COMPARISON WITH THE G(SLASH)*A MISMATCH' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D62 _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 2 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _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 hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DG 10 N1 ? ? A DC 1 A DG 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 10 O6 ? ? A DC 1 A DG 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 10 N2 ? ? A DC 1 A DG 10 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 2 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 2 A DG 9 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 2 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 2 A DG 9 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 2 A DG 9 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 8 N3 ? ? A DA 3 A DT 8 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 8 O4 ? ? A DA 3 A DT 8 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 A DT 7 N3 ? ? A DA 4 A DT 7 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 A DT 7 O4 ? ? A DA 4 A DT 7 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 7 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 7 A DA 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DT 7 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 7 A DA 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DT 8 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 8 A DA 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 8 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 8 A DA 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 10 O6 ? ? ? 1_555 A DC 1 N4 ? ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1D62 _database_PDB_matrix.origx[1][1] 0.908503 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.417865 _database_PDB_matrix.origx_vector[1] 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_vector[2] 0.000000 _database_PDB_matrix.origx[3][1] -0.417853 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 0.908520 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 1D62 _atom_sites.fract_transf_matrix[1][1] 0.031046 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.014280 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.039777 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_vector[2] 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] 0.032241 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C 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 DC 1 1 1 DC C A . n A 1 2 DC 2 2 2 DC C A . n A 1 3 DA 3 3 3 DA A A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DI 5 5 5 DI I A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DG 10 10 10 DG G A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 11 11 HOH HOH A . B 2 HOH 2 12 12 HOH HOH A . B 2 HOH 3 13 13 HOH HOH A . B 2 HOH 4 14 14 HOH HOH A . B 2 HOH 5 15 15 HOH HOH A . B 2 HOH 6 16 16 HOH HOH A . B 2 HOH 7 17 17 HOH HOH A . B 2 HOH 8 18 18 HOH HOH A . B 2 HOH 9 19 19 HOH HOH A . B 2 HOH 10 20 20 HOH HOH A . B 2 HOH 11 21 21 HOH HOH A . B 2 HOH 12 22 22 HOH HOH A . B 2 HOH 13 23 23 HOH HOH A . B 2 HOH 14 24 24 HOH HOH A . B 2 HOH 15 25 25 HOH HOH A . B 2 HOH 16 26 26 HOH HOH A . B 2 HOH 17 27 27 HOH HOH A . B 2 HOH 18 28 28 HOH HOH A . B 2 HOH 19 29 29 HOH HOH A . B 2 HOH 20 30 30 HOH HOH A . B 2 HOH 21 31 31 HOH HOH A . B 2 HOH 22 32 32 HOH HOH A . B 2 HOH 23 33 33 HOH HOH A . B 2 HOH 24 34 34 HOH HOH A . B 2 HOH 25 35 35 HOH HOH A . B 2 HOH 26 36 36 HOH HOH A . B 2 HOH 27 37 37 HOH HOH A . B 2 HOH 28 38 38 HOH HOH A . B 2 HOH 29 39 39 HOH HOH A . B 2 HOH 30 40 40 HOH HOH A . B 2 HOH 31 41 41 HOH HOH A . B 2 HOH 32 42 42 HOH HOH A . B 2 HOH 33 43 43 HOH HOH A . B 2 HOH 34 44 44 HOH HOH A . B 2 HOH 35 45 45 HOH HOH A . B 2 HOH 36 46 46 HOH HOH A . B 2 HOH 37 47 47 HOH HOH A . B 2 HOH 38 48 48 HOH HOH A . B 2 HOH 39 49 49 HOH HOH A . B 2 HOH 40 50 50 HOH HOH A . B 2 HOH 41 51 51 HOH HOH A . B 2 HOH 42 52 52 HOH HOH A . B 2 HOH 43 53 53 HOH HOH A . B 2 HOH 44 54 54 HOH HOH A . B 2 HOH 45 55 55 HOH HOH A . B 2 HOH 46 56 56 HOH HOH A . B 2 HOH 47 57 57 HOH HOH A . B 2 HOH 48 58 58 HOH HOH A . B 2 HOH 49 59 59 HOH HOH A . B 2 HOH 50 60 60 HOH HOH A . # _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 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 2_555 -x,y,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 12 ? B HOH . 2 1 A HOH 13 ? B HOH . # 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 1993-07-15 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 2 0 2023-07-26 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 4 'Structure model' repository Remediation ? 'Coordinates and associated ncs operations (if present) transformed into standard crystal frame' # 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' Advisory 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' Advisory 5 4 'Structure model' 'Atomic model' 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' 8 4 'Structure model' 'Derived calculations' 9 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' atom_site 2 4 'Structure model' atom_sites 3 4 'Structure model' database_2 4 4 'Structure model' database_PDB_matrix 5 4 'Structure model' pdbx_database_remark 6 4 'Structure model' pdbx_struct_special_symmetry 7 4 'Structure model' pdbx_validate_rmsd_angle # 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' '_atom_site.Cartn_x' 2 4 'Structure model' '_atom_site.Cartn_z' 3 4 'Structure model' '_atom_site.occupancy' 4 4 'Structure model' '_atom_sites.fract_transf_matrix[1][1]' 5 4 'Structure model' '_atom_sites.fract_transf_matrix[1][3]' 6 4 'Structure model' '_atom_sites.fract_transf_matrix[3][1]' 7 4 'Structure model' '_atom_sites.fract_transf_matrix[3][3]' 8 4 'Structure model' '_database_2.pdbx_DOI' 9 4 'Structure model' '_database_2.pdbx_database_accession' 10 4 'Structure model' '_database_PDB_matrix.origx[1][1]' 11 4 'Structure model' '_database_PDB_matrix.origx[1][3]' 12 4 'Structure model' '_database_PDB_matrix.origx[3][1]' 13 4 'Structure model' '_database_PDB_matrix.origx[3][3]' 14 4 'Structure model' '_pdbx_validate_rmsd_angle.angle_deviation' 15 4 'Structure model' '_pdbx_validate_rmsd_angle.angle_value' # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # 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 "O4'" A DC 2 ? ? "C4'" A DC 2 ? ? 1.384 1.446 -0.062 0.010 N 2 1 N3 A DC 2 ? ? C4 A DC 2 ? ? 1.381 1.335 0.046 0.007 N 3 1 P A DG 10 ? ? "O5'" A DG 10 ? ? 1.669 1.593 0.076 0.010 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 DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 101.36 108.00 -6.64 0.70 N 2 1 "O5'" A DC 2 ? ? "C5'" A DC 2 ? ? "C4'" A DC 2 ? ? 102.51 109.40 -6.89 0.80 N 3 1 "O4'" A DC 2 ? ? "C1'" A DC 2 ? ? "C2'" A DC 2 ? ? 100.96 105.90 -4.94 0.80 N 4 1 N1 A DC 2 ? ? C2 A DC 2 ? ? O2 A DC 2 ? ? 122.89 118.90 3.99 0.60 N 5 1 "C3'" A DC 2 ? ? "O3'" A DC 2 ? ? P A DA 3 ? ? 133.49 119.70 13.79 1.20 Y 6 1 OP1 A DA 3 ? ? P A DA 3 ? ? OP2 A DA 3 ? ? 110.49 119.60 -9.11 1.50 N 7 1 "O5'" A DA 3 ? ? "C5'" A DA 3 ? ? "C4'" A DA 3 ? ? 103.93 109.40 -5.47 0.80 N 8 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 99.09 108.00 -8.91 0.70 N 9 1 C5 A DA 3 ? ? C6 A DA 3 ? ? N1 A DA 3 ? ? 113.80 117.70 -3.90 0.50 N 10 1 N1 A DA 3 ? ? C6 A DA 3 ? ? N6 A DA 3 ? ? 127.15 118.60 8.55 0.60 N 11 1 "O5'" A DA 4 ? ? P A DA 4 ? ? OP1 A DA 4 ? ? 121.32 110.70 10.62 1.20 N 12 1 "O5'" A DA 4 ? ? "C5'" A DA 4 ? ? "C4'" A DA 4 ? ? 103.13 109.40 -6.27 0.80 N 13 1 "C3'" A DA 4 ? ? "C2'" A DA 4 ? ? "C1'" A DA 4 ? ? 96.91 102.40 -5.49 0.80 N 14 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 118.55 108.30 10.25 0.30 N 15 1 N1 A DA 4 ? ? C2 A DA 4 ? ? N3 A DA 4 ? ? 123.62 129.30 -5.68 0.50 N 16 1 C2 A DA 4 ? ? N3 A DA 4 ? ? C4 A DA 4 ? ? 113.81 110.60 3.21 0.50 N 17 1 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 122.47 118.60 3.87 0.60 N 18 1 "C3'" A DI 5 ? ? "O3'" A DI 5 ? ? P A DA 6 ? ? 111.03 119.70 -8.67 1.20 Y 19 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 111.27 108.30 2.97 0.30 N 20 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 123.68 118.60 5.08 0.60 N 21 1 N1 A DA 6 ? ? C2 A DA 6 ? ? N3 A DA 6 ? ? 125.83 129.30 -3.47 0.50 N 22 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N1 A DA 6 ? ? 113.86 117.70 -3.84 0.50 N 23 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 103.00 109.40 -6.40 0.80 N 24 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 101.31 108.00 -6.69 0.70 N 25 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 121.14 127.20 -6.06 0.60 N 26 1 N3 A DT 7 ? ? C4 A DT 7 ? ? C5 A DT 7 ? ? 119.71 115.20 4.51 0.60 N 27 1 N3 A DT 7 ? ? C2 A DT 7 ? ? O2 A DT 7 ? ? 114.30 122.30 -8.00 0.60 N 28 1 N3 A DT 7 ? ? C4 A DT 7 ? ? O4 A DT 7 ? ? 111.84 119.90 -8.06 0.60 N 29 1 "O5'" A DT 8 ? ? "C5'" A DT 8 ? ? "C4'" A DT 8 ? ? 101.69 109.40 -7.71 0.80 N 30 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? "C2'" A DT 8 ? ? 98.67 105.90 -7.23 0.80 N 31 1 N1 A DT 8 ? ? C2 A DT 8 ? ? N3 A DT 8 ? ? 118.97 114.60 4.37 0.60 N 32 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 120.72 127.20 -6.48 0.60 N 33 1 N3 A DT 8 ? ? C4 A DT 8 ? ? C5 A DT 8 ? ? 120.20 115.20 5.00 0.60 N 34 1 "C3'" A DT 8 ? ? "O3'" A DT 8 ? ? P A DG 9 ? ? 126.92 119.70 7.22 1.20 Y 35 1 "C5'" A DG 9 ? ? "C4'" A DG 9 ? ? "O4'" A DG 9 ? ? 118.39 109.80 8.59 1.10 N 36 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 102.89 108.00 -5.11 0.70 N 37 1 "O5'" A DG 10 ? ? "C5'" A DG 10 ? ? "C4'" A DG 10 ? ? 102.74 109.40 -6.66 0.80 N 38 1 P A DG 10 ? ? "O5'" A DG 10 ? ? "C5'" A DG 10 ? ? 103.85 120.90 -17.05 1.60 N 39 1 "C1'" A DG 10 ? ? "O4'" A DG 10 ? ? "C4'" A DG 10 ? ? 103.17 110.10 -6.93 1.00 N 40 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 114.65 111.50 3.15 0.50 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1D62 'b-form double helix' 1D62 'internal loop' # 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 DC 1 1_555 A DG 10 2_555 0.096 -0.058 0.381 -9.202 -11.284 0.520 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 2_555 -0.048 -0.277 0.117 -4.671 -11.100 -4.335 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 2_555 -0.049 -0.255 0.342 -2.141 -6.374 0.843 3 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DA 4 1_555 A DT 7 2_555 -0.654 -0.350 0.097 0.275 -15.545 1.011 4 A_DA4:DT7_A A 4 ? A 7 ? 20 1 1 A DC 1 1_555 A DG 10 1_555 0.096 -0.058 0.381 -9.202 -11.284 0.520 5 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 1_555 -0.048 -0.277 0.117 -4.671 -11.100 -4.335 6 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 1_555 -0.049 -0.255 0.342 -2.141 -6.374 0.843 7 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DA 4 1_555 A DT 7 1_555 -0.654 -0.350 0.097 0.275 -15.545 1.011 8 A_DA4:DT7_A A 4 ? A 7 ? 20 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 A DG 10 2_555 A DC 2 1_555 A DG 9 2_555 -0.822 0.602 3.183 2.538 5.234 27.729 0.044 2.255 3.154 10.772 -5.223 28.321 1 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 2_555 A DA 3 1_555 A DT 8 2_555 0.168 2.770 3.278 -4.072 -10.761 54.210 3.568 -0.402 2.707 -11.661 4.412 55.327 2 AA_DC2DA3:DT8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DA 3 1_555 A DT 8 2_555 A DA 4 1_555 A DT 7 2_555 0.633 0.290 3.335 1.493 8.512 22.000 -2.255 -1.028 3.252 21.279 -3.731 23.617 3 AA_DA3DA4:DT7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DC 1 1_555 A DG 10 1_555 A DC 2 1_555 A DG 9 1_555 -0.822 0.602 3.183 2.538 5.234 27.729 0.044 2.255 3.154 10.772 -5.223 28.321 4 AA_DC1DC2:DG9DG10_AA A 1 ? A 10 ? A 2 ? A 9 ? 1 A DC 2 1_555 A DG 9 1_555 A DA 3 1_555 A DT 8 1_555 0.168 2.770 3.278 -4.072 -10.761 54.210 3.568 -0.402 2.707 -11.661 4.412 55.327 5 AA_DC2DA3:DT8DG9_AA A 2 ? A 9 ? A 3 ? A 8 ? 1 A DA 3 1_555 A DT 8 1_555 A DA 4 1_555 A DT 7 1_555 0.633 0.290 3.335 1.493 8.512 22.000 -2.255 -1.028 3.252 21.279 -3.731 23.617 6 AA_DA3DA4:DT7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #