data_1D61 # _entry.id 1D61 # _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 1D61 pdb_00001d61 10.2210/pdb1d61/pdb RCSB BDJB44 ? ? WWPDB D_1000172662 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D61 _pdbx_database_status.recvd_initial_deposition_date 1992-02-26 _pdbx_database_status.deposit_site BNL _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 'Quintana, J.' 4 'Dickerson, R.E.' 5 # 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 'Helix Geometry, Hydration, and G.A Mismatch in a B-DNA Decamer' Science 238 498 504 1992 SCIEAS US 0036-8075 0038 ? ? ? 2 'Crystallographic Study of One Turn of G/C-Rich B-DNA' J.Mol.Biol. 210 369 381 1992 JMOBAK UK 0022-2836 0070 ? ? ? 3 ;Structure of the B-DNA Decamer C-C-A-A-C-G-T-T-G-G and Comparison with 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 1992 JMOBAK UK 0022-2836 0070 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lipanov, A.' 1 ? primary 'Kopka, M.L.' 2 ? primary 'Kaczor-Grzeskowiak, M.' 3 ? primary 'Quintana, J.' 4 ? primary 'Dickerson, R.E.' 5 ? 1 'Prive, G.G.' 6 ? 1 'Heinemann, U.' 7 ? 1 'Chandrasegaran, S.' 8 ? 1 'Kan, L.S.' 9 ? 1 'Kopka, M.L.' 10 ? 1 'Dickerson, R.E.' 11 ? 2 'Heinemann, U.' 12 ? 2 'Alings, C.' 13 ? 3 'Prive, G.G.' 14 ? 3 'Yanagi, K.' 15 ? 3 'Dickerson, R.E.' 16 ? # _cell.entry_id 1D61 _cell.length_a 31.870 _cell.length_b 25.690 _cell.length_c 34.210 _cell.angle_alpha 90.00 _cell.angle_beta 114.10 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D61 _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 ;DNA (5'-D(*CP*CP*AP*AP*CP*IP*TP*TP*GP*G)-3') ; 3029.990 1 ? ? ? ? 2 non-polymer syn 'CACODYLATE ION' 136.989 1 ? ? ? ? 3 non-polymer syn 'CALCIUM ION' 40.078 1 ? ? ? ? 4 water nat water 18.015 79 ? ? ? ? # _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)(DC)(DI)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAACITTGG _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 DC n 1 6 DI 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 1D61 _struct_ref.pdbx_db_accession 1D61 _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 1D61 _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 1D61 _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 CA non-polymer . 'CALCIUM ION' ? 'Ca 2' 40.078 CAC non-polymer . 'CACODYLATE ION' dimethylarsinate 'C2 H6 As O2 -1' 136.989 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 1D61 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 39.23 _exptl_crystal.density_Matthews 2.02 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.10 _exptl_crystal_grow.pdbx_details 'pH 7.10, VAPOR DIFFUSION, SITTING DROP, temperature 277.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? 1 3 1 'CA CACODYLATE' ? ? ? 1 4 1 'NA CACODYLATE' ? ? ? 1 5 1 SPERMIDINE ? ? ? 1 6 2 WATER ? ? ? 1 7 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 248.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'RIGAKU AFC-5R' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _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 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1D61 _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 8.000 _reflns.d_resolution_high 1.300 _reflns.number_obs 5026 _reflns.number_all 5848 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _refine.entry_id 1D61 _refine.ls_number_reflns_obs 5026 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 1.300 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1520000 _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 201 _refine_hist.pdbx_number_atoms_ligand 4 _refine_hist.number_atoms_solvent 79 _refine_hist.number_atoms_total 284 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low 8.000 # _struct.entry_id 1D61 _struct.title 'THE STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G: MONOCLINIC FORM' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D61 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, MODIFIED, 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 ? C N N 3 ? D N N 4 ? # _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 metalc1 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 85 1_555 ? ? ? ? ? ? ? 2.417 ? ? metalc2 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 86 1_555 ? ? ? ? ? ? ? 2.519 ? ? metalc3 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 87 1_555 ? ? ? ? ? ? ? 2.462 ? ? metalc4 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 88 1_555 ? ? ? ? ? ? ? 2.479 ? ? metalc5 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 89 1_555 ? ? ? ? ? ? ? 2.318 ? ? metalc6 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 90 1_555 ? ? ? ? ? ? ? 2.625 ? ? metalc7 metalc ? ? C CA . CA ? ? ? 1_555 D HOH . O ? ? A CA 12 A HOH 91 1_555 ? ? ? ? ? ? ? 2.406 ? ? 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 ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A CAC 11 ? 9 'BINDING SITE FOR RESIDUE CAC A 11' AC2 Software A CA 12 ? 7 'BINDING SITE FOR RESIDUE CA A 12' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 9 DC A 1 ? DC A 1 . ? 1_554 ? 2 AC1 9 DC A 2 ? DC A 2 . ? 2_556 ? 3 AC1 9 HOH D . ? HOH A 24 . ? 3_556 ? 4 AC1 9 HOH D . ? HOH A 24 . ? 4_455 ? 5 AC1 9 HOH D . ? HOH A 29 . ? 3_556 ? 6 AC1 9 HOH D . ? HOH A 33 . ? 1_555 ? 7 AC1 9 HOH D . ? HOH A 34 . ? 2_556 ? 8 AC1 9 HOH D . ? HOH A 34 . ? 1_555 ? 9 AC1 9 HOH D . ? HOH A 44 . ? 4_454 ? 10 AC2 7 HOH D . ? HOH A 85 . ? 1_555 ? 11 AC2 7 HOH D . ? HOH A 86 . ? 1_555 ? 12 AC2 7 HOH D . ? HOH A 87 . ? 1_555 ? 13 AC2 7 HOH D . ? HOH A 88 . ? 1_555 ? 14 AC2 7 HOH D . ? HOH A 89 . ? 1_555 ? 15 AC2 7 HOH D . ? HOH A 90 . ? 1_555 ? 16 AC2 7 HOH D . ? HOH A 91 . ? 1_555 ? # _database_PDB_matrix.entry_id 1D61 _database_PDB_matrix.origx[1][1] 0.912826 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.408327 _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] -0.408337 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 0.912839 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 1D61 _atom_sites.fract_transf_matrix[1][1] 0.031377 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.014036 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.038926 _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] 0.032022 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol AS C CA 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 DC 5 5 5 DC C A . n A 1 6 DI 6 6 6 DI I 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 CAC 1 11 11 CAC CAC A . C 3 CA 1 12 12 CA OC7 A . D 4 HOH 1 13 13 HOH HOH A . D 4 HOH 2 14 14 HOH HOH A . D 4 HOH 3 15 15 HOH HOH A . D 4 HOH 4 16 16 HOH HOH A . D 4 HOH 5 17 17 HOH HOH A . D 4 HOH 6 18 18 HOH HOH A . D 4 HOH 7 19 19 HOH HOH A . D 4 HOH 8 20 20 HOH HOH A . D 4 HOH 9 21 21 HOH HOH A . D 4 HOH 10 22 22 HOH HOH A . D 4 HOH 11 23 23 HOH HOH A . D 4 HOH 12 24 24 HOH HOH A . D 4 HOH 13 25 25 HOH HOH A . D 4 HOH 14 26 26 HOH HOH A . D 4 HOH 15 27 27 HOH HOH A . D 4 HOH 16 28 28 HOH HOH A . D 4 HOH 17 29 29 HOH HOH A . D 4 HOH 18 30 30 HOH HOH A . D 4 HOH 19 31 31 HOH HOH A . D 4 HOH 20 32 32 HOH HOH A . D 4 HOH 21 33 33 HOH HOH A . D 4 HOH 22 34 34 HOH HOH A . D 4 HOH 23 35 35 HOH HOH A . D 4 HOH 24 36 36 HOH HOH A . D 4 HOH 25 37 37 HOH HOH A . D 4 HOH 26 38 38 HOH HOH A . D 4 HOH 27 39 39 HOH HOH A . D 4 HOH 28 40 40 HOH HOH A . D 4 HOH 29 41 41 HOH HOH A . D 4 HOH 30 42 42 HOH HOH A . D 4 HOH 31 43 43 HOH HOH A . D 4 HOH 32 44 44 HOH HOH A . D 4 HOH 33 45 45 HOH HOH A . D 4 HOH 34 46 46 HOH HOH A . D 4 HOH 35 47 47 HOH HOH A . D 4 HOH 36 48 48 HOH HOH A . D 4 HOH 37 49 49 HOH HOH A . D 4 HOH 38 50 50 HOH HOH A . D 4 HOH 39 51 51 HOH HOH A . D 4 HOH 40 52 52 HOH HOH A . D 4 HOH 41 53 53 HOH HOH A . D 4 HOH 42 54 54 HOH HOH A . D 4 HOH 43 55 55 HOH HOH A . D 4 HOH 44 56 56 HOH HOH A . D 4 HOH 45 57 57 HOH HOH A . D 4 HOH 46 58 58 HOH HOH A . D 4 HOH 47 59 59 HOH HOH A . D 4 HOH 48 60 60 HOH HOH A . D 4 HOH 49 61 61 HOH HOH A . D 4 HOH 50 62 62 HOH HOH A . D 4 HOH 51 63 63 HOH HOH A . D 4 HOH 52 64 64 HOH HOH A . D 4 HOH 53 65 65 HOH HOH A . D 4 HOH 54 66 66 HOH HOH A . D 4 HOH 55 67 67 HOH HOH A . D 4 HOH 56 68 68 HOH HOH A . D 4 HOH 57 69 69 HOH HOH A . D 4 HOH 58 70 70 HOH HOH A . D 4 HOH 59 71 71 HOH HOH A . D 4 HOH 60 72 72 HOH HOH A . D 4 HOH 61 73 73 HOH HOH A . D 4 HOH 62 74 74 HOH HOH A . D 4 HOH 63 75 75 HOH HOH A . D 4 HOH 64 76 76 HOH HOH A . D 4 HOH 65 77 77 HOH HOH A . D 4 HOH 66 78 78 HOH HOH A . D 4 HOH 67 79 79 HOH HOH A . D 4 HOH 68 80 80 HOH HOH A . D 4 HOH 69 81 81 HOH HOH A . D 4 HOH 70 82 82 HOH HOH A . D 4 HOH 71 83 83 HOH HOH A . D 4 HOH 72 84 84 HOH HOH A . D 4 HOH 73 85 12 HOH OC7 A . D 4 HOH 74 86 12 HOH OC7 A . D 4 HOH 75 87 12 HOH OC7 A . D 4 HOH 76 88 12 HOH OC7 A . D 4 HOH 77 89 12 HOH OC7 A . D 4 HOH 78 90 12 HOH OC7 A . D 4 HOH 79 91 12 HOH OC7 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,C,D # 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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 13 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id D _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 O ? D HOH . ? A HOH 85 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 86 ? 1_555 91.4 ? 2 O ? D HOH . ? A HOH 85 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 87 ? 1_555 104.7 ? 3 O ? D HOH . ? A HOH 86 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 87 ? 1_555 74.6 ? 4 O ? D HOH . ? A HOH 85 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 88 ? 1_555 88.6 ? 5 O ? D HOH . ? A HOH 86 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 88 ? 1_555 141.3 ? 6 O ? D HOH . ? A HOH 87 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 88 ? 1_555 142.3 ? 7 O ? D HOH . ? A HOH 85 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 89 ? 1_555 78.7 ? 8 O ? D HOH . ? A HOH 86 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 89 ? 1_555 137.8 ? 9 O ? D HOH . ? A HOH 87 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 89 ? 1_555 68.8 ? 10 O ? D HOH . ? A HOH 88 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 89 ? 1_555 80.0 ? 11 O ? D HOH . ? A HOH 85 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 90 ? 1_555 85.0 ? 12 O ? D HOH . ? A HOH 86 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 90 ? 1_555 69.0 ? 13 O ? D HOH . ? A HOH 87 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 90 ? 1_555 142.5 ? 14 O ? D HOH . ? A HOH 88 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 90 ? 1_555 72.4 ? 15 O ? D HOH . ? A HOH 89 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 90 ? 1_555 148.2 ? 16 O ? D HOH . ? A HOH 85 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 91 ? 1_555 172.8 ? 17 O ? D HOH . ? A HOH 86 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 91 ? 1_555 87.3 ? 18 O ? D HOH . ? A HOH 87 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 91 ? 1_555 81.8 ? 19 O ? D HOH . ? A HOH 88 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 91 ? 1_555 87.9 ? 20 O ? D HOH . ? A HOH 89 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 91 ? 1_555 106.9 ? 21 O ? D HOH . ? A HOH 90 ? 1_555 CA ? C CA . ? A CA 12 ? 1_555 O ? D HOH . ? A HOH 91 ? 1_555 87.9 ? # 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 1993-04-15 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_struct_conn_angle 6 4 'Structure model' pdbx_validate_rmsd_angle 7 4 'Structure model' pdbx_validate_rmsd_bond 8 4 'Structure model' pdbx_validate_symm_contact 9 4 'Structure model' struct_conn 10 4 'Structure model' struct_site # 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_struct_conn_angle.ptnr1_auth_seq_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.value' 17 4 'Structure model' '_pdbx_validate_rmsd_angle.angle_deviation' 18 4 'Structure model' '_pdbx_validate_rmsd_angle.angle_value' 19 4 'Structure model' '_pdbx_validate_rmsd_bond.bond_deviation' 20 4 'Structure model' '_pdbx_validate_rmsd_bond.bond_value' 21 4 'Structure model' '_pdbx_validate_symm_contact.site_symmetry_2' 22 4 'Structure model' '_struct_conn.pdbx_dist_value' 23 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 24 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 25 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 26 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL IONS' TR isotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL IONS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _pdbx_database_remark.id 285 _pdbx_database_remark.text ;THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME. ; # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 14 ? ? 1_555 O A HOH 14 ? ? 2_554 1.70 2 1 O2 A CAC 11 ? ? 1_555 O A HOH 44 ? ? 3_556 2.19 # 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 P A DC 2 ? ? OP1 A DC 2 ? ? 1.376 1.485 -0.109 0.017 N 2 1 P A DC 2 ? ? OP2 A DC 2 ? ? 1.249 1.485 -0.236 0.017 N 3 1 P A DC 2 ? ? "O5'" A DC 2 ? ? 1.682 1.593 0.089 0.010 N 4 1 P A DC 5 ? ? "O5'" A DC 5 ? ? 1.660 1.593 0.067 0.010 N 5 1 "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 1.383 1.446 -0.063 0.010 N 6 1 P A DT 8 ? ? OP2 A DT 8 ? ? 1.352 1.485 -0.133 0.017 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 "O5'" A DC 1 ? ? "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? 102.31 109.40 -7.09 0.80 N 2 1 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? "C3'" A DC 1 ? ? 125.27 115.70 9.57 1.20 N 3 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 101.63 108.00 -6.37 0.70 N 4 1 "O3'" A DC 1 ? ? P A DC 2 ? ? OP2 A DC 2 ? ? 121.02 110.50 10.52 1.10 Y 5 1 C2 A DC 2 ? ? N3 A DC 2 ? ? C4 A DC 2 ? ? 123.43 119.90 3.53 0.50 N 6 1 C5 A DC 2 ? ? C6 A DC 2 ? ? N1 A DC 2 ? ? 124.76 121.00 3.76 0.50 N 7 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 101.69 108.00 -6.31 0.70 N 8 1 C6 A DA 3 ? ? N1 A DA 3 ? ? C2 A DA 3 ? ? 124.00 118.60 5.40 0.60 N 9 1 N1 A DA 3 ? ? C2 A DA 3 ? ? N3 A DA 3 ? ? 123.42 129.30 -5.88 0.50 N 10 1 "C3'" A DA 3 ? ? "O3'" A DA 3 ? ? P A DA 4 ? ? 127.34 119.70 7.64 1.20 Y 11 1 "O4'" A DA 4 ? ? "C1'" A DA 4 ? ? N9 A DA 4 ? ? 103.58 108.00 -4.42 0.70 N 12 1 C5 A DA 4 ? ? C6 A DA 4 ? ? N1 A DA 4 ? ? 113.16 117.70 -4.54 0.50 N 13 1 "O5'" A DC 5 ? ? "C5'" A DC 5 ? ? "C4'" A DC 5 ? ? 103.46 109.40 -5.94 0.80 N 14 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.34 108.30 3.04 0.30 N 15 1 C2 A DC 5 ? ? N3 A DC 5 ? ? C4 A DC 5 ? ? 125.33 119.90 5.43 0.50 N 16 1 N3 A DC 5 ? ? C4 A DC 5 ? ? C5 A DC 5 ? ? 117.02 121.90 -4.88 0.40 N 17 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 102.82 109.40 -6.58 0.80 N 18 1 OP1 A DT 8 ? ? P A DT 8 ? ? OP2 A DT 8 ? ? 130.00 119.60 10.40 1.50 N 19 1 "O5'" A DT 8 ? ? "C5'" A DT 8 ? ? "C4'" A DT 8 ? ? 104.10 109.40 -5.30 0.80 N 20 1 N1 A DT 8 ? ? C2 A DT 8 ? ? N3 A DT 8 ? ? 118.97 114.60 4.37 0.60 N 21 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 120.86 127.20 -6.34 0.60 N 22 1 C5 A DT 8 ? ? C6 A DT 8 ? ? N1 A DT 8 ? ? 119.09 123.70 -4.61 0.60 N 23 1 N3 A DT 8 ? ? C2 A DT 8 ? ? O2 A DT 8 ? ? 118.18 122.30 -4.12 0.60 N 24 1 C6 A DT 8 ? ? C5 A DT 8 ? ? C7 A DT 8 ? ? 119.04 122.90 -3.86 0.60 N 25 1 C6 A DG 9 ? ? N1 A DG 9 ? ? C2 A DG 9 ? ? 119.34 125.10 -5.76 0.60 N 26 1 C5 A DG 9 ? ? C6 A DG 9 ? ? N1 A DG 9 ? ? 117.76 111.50 6.26 0.50 N 27 1 N1 A DG 9 ? ? C6 A DG 9 ? ? O6 A DG 9 ? ? 116.24 119.90 -3.66 0.60 N 28 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 103.24 108.00 -4.76 0.70 N 29 1 C2 A DG 10 ? ? N3 A DG 10 ? ? C4 A DG 10 ? ? 115.81 111.90 3.91 0.50 N 30 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 116.55 111.50 5.05 0.50 N 31 1 C4 A DG 10 ? ? C5 A DG 10 ? ? N7 A DG 10 ? ? 107.80 110.80 -3.00 0.40 N 32 1 C5 A DG 10 ? ? N7 A DG 10 ? ? C8 A DG 10 ? ? 107.53 104.30 3.23 0.50 N 33 1 C6 A DG 10 ? ? C5 A DG 10 ? ? N7 A DG 10 ? ? 136.02 130.40 5.62 0.60 N 34 1 N1 A DG 10 ? ? C6 A DG 10 ? ? O6 A DG 10 ? ? 114.53 119.90 -5.37 0.60 N # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 N 1 A CAC 11 ? C1 ? B CAC 1 C1 2 1 N 1 A CAC 11 ? C2 ? B CAC 1 C2 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1D61 'b-form double helix' 1D61 '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 0.160 -0.082 0.132 -8.515 -13.262 2.252 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 2_555 0.308 -0.176 0.046 -0.756 -11.248 -1.421 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 2_555 0.003 -0.119 0.234 1.788 -5.383 -0.482 3 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DA 4 1_555 A DT 7 2_555 -0.019 -0.125 0.149 2.186 -14.336 4.449 4 A_DA4:DT7_A A 4 ? A 7 ? 20 1 1 A DC 1 1_555 A DG 10 1_555 0.160 -0.082 0.132 -8.515 -13.262 2.252 5 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 1_555 0.308 -0.176 0.046 -0.756 -11.248 -1.421 6 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 1_555 0.003 -0.119 0.234 1.787 -5.383 -0.482 7 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DA 4 1_555 A DT 7 1_555 -0.019 -0.125 0.149 2.186 -14.336 4.449 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 -0.669 0.768 3.153 2.740 9.378 28.091 -0.460 1.877 3.162 18.621 -5.441 29.710 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 0.273 2.806 3.227 -1.685 -9.943 49.919 3.899 -0.425 2.649 -11.644 1.973 50.864 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 0.390 0.110 3.412 -1.344 10.417 27.944 -2.063 -1.053 3.223 20.669 2.666 29.816 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 -0.669 0.768 3.153 2.740 9.378 28.091 -0.460 1.877 3.162 18.622 -5.441 29.710 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 0.273 2.806 3.227 -1.685 -9.943 49.919 3.899 -0.425 2.649 -11.644 1.973 50.864 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 0.390 0.110 3.412 -1.344 10.416 27.944 -2.063 -1.053 3.223 20.669 2.666 29.816 6 AA_DA3DA4:DT7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CACODYLATE ION' CAC 3 'CALCIUM ION' CA 4 water HOH #