data_1D79 # _entry.id 1D79 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.367 _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 1D79 pdb_00001d79 10.2210/pdb1d79/pdb RCSB ADH039 ? ? WWPDB D_1000172677 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1D79 _pdbx_database_status.recvd_initial_deposition_date 1992-06-12 _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 _audit_author.identifier_ORCID 'Thota, N.' 1 ? 'Li, X.H.' 2 ? 'Bingman, C.A.' 3 ? 'Sundaralingam, M.' 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 'High-resolution refinement of the hexagonal A-DNA octamer d(GTGTACAC) at 1.4 A.' 'Acta Crystallogr.,Sect.D' 49 282 291 1993 ABCRE6 DK 0907-4449 0766 ? 15299533 10.1107/S0907444992007522 1 ;Hexagonal Crystal Structure of the A-DNA Octamer d(GTGTACAC) and Its Comparison with the Tetragonal Structure: Correlated Variations in Helical Parameters ; Biochemistry 30 3567 3576 1991 BICHAW US 0006-2960 0033 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Thota, N.' 1 ? primary 'Li, X.H.' 2 ? primary 'Bingman, C.A.' 3 ? primary 'Sundaralingam, M.' 4 ? 1 'Jain, S.' 5 ? 1 'Zon, G.' 6 ? 1 'Sundaralingam, M.' 7 ? # _cell.entry_id 1D79 _cell.length_a 32.341 _cell.length_b 32.341 _cell.length_c 78.490 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D79 _symmetry.space_group_name_H-M 'P 61 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 # 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(*GP*TP*GP*TP*AP*CP*AP*C)-3') ; 2426.617 1 ? ? ? ? 2 water nat water 18.015 35 ? ? ? ? # _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 '(DG)(DT)(DG)(DT)(DA)(DC)(DA)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GTGTACAC _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 DG n 1 2 DT n 1 3 DG n 1 4 DT n 1 5 DA n 1 6 DC n 1 7 DA n 1 8 DC n # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1D79 _struct_ref.pdbx_db_accession 1D79 _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 1D79 _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 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 1D79 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _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 8 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 # _exptl.entry_id 1D79 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.44 _exptl_crystal.density_percent_sol 49.62 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 283.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'VAPOR DIFFUSION, temperature 283.00K' _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 MGCL2 ? ? ? 1 4 1 SPERMIDINE ? ? ? 1 5 2 WATER ? ? ? 1 6 2 MPD ? ? ? 1 7 2 MGCL2 ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 258.00 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'AREA DETECTOR' _diffrn_detector.type XENTRONICS _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 ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _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 ? _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 1D79 _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 5.000 _reflns.d_resolution_high 1.450 _reflns.number_obs 3292 _reflns.number_all 6017 _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.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_CC_star ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_Rrim_I_all ? # _refine.entry_id 1D79 _refine.ls_number_reflns_obs 3292 _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 5.000 _refine.ls_d_res_high 1.450 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1910000 _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.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 161 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 35 _refine_hist.number_atoms_total 196 _refine_hist.d_res_high 1.450 _refine_hist.d_res_low 5.000 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function n_bond_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_planar_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_hb_or_metal_coord ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_angle_it ? ? ? ? 'X-RAY DIFFRACTION' ? n_bond_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_dihedral_angle_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_impr_tor ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_d 0.004 ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d 0.043 ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_plane_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_chiral_restr ? ? ? ? 'X-RAY DIFFRACTION' ? n_singtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_multtor_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? n_xhyhbond_nbd ? ? ? ? 'X-RAY DIFFRACTION' ? # _struct.entry_id 1D79 _struct.title 'HIGH RESOLUTION REFINEMENT OF THE HEXAGONAL A-DNA OCTAMER D(GTGTACAC) AT 1.4 ANGSTROMS RESOLUTION' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1D79 _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'A-DNA, DOUBLE HELIX, 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 ? # 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 DG 1 N1 ? ? ? 1_555 A DC 8 N3 ? ? A DG 1 A DC 8 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 8 O2 ? ? A DG 1 A DC 8 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 8 N4 ? ? A DG 1 A DC 8 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 2 N3 ? ? ? 1_555 A DA 7 N1 ? ? A DT 2 A DA 7 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 2 O4 ? ? ? 1_555 A DA 7 N6 ? ? A DT 2 A DA 7 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 3 N1 ? ? ? 1_555 A DC 6 N3 ? ? A DG 3 A DC 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DG 3 N2 ? ? ? 1_555 A DC 6 O2 ? ? A DG 3 A DC 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DG 3 O6 ? ? ? 1_555 A DC 6 N4 ? ? A DG 3 A DC 6 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DT 4 N3 ? ? ? 1_555 A DA 5 N1 ? ? A DT 4 A DA 5 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 O4 ? ? ? 1_555 A DA 5 N6 ? ? A DT 4 A DA 5 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DA 5 N1 ? ? ? 1_555 A DT 4 N3 ? ? A DA 5 A DT 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N6 ? ? ? 1_555 A DT 4 O4 ? ? A DA 5 A DT 4 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 6 N3 ? ? ? 1_555 A DG 3 N1 ? ? A DC 6 A DG 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 6 N4 ? ? ? 1_555 A DG 3 O6 ? ? A DC 6 A DG 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 3 N2 ? ? A DC 6 A DG 3 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 A DT 2 N3 ? ? A DA 7 A DT 2 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 A DT 2 O4 ? ? A DA 7 A DT 2 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 8 A DG 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 8 A DG 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 8 A DG 1 12_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _database_PDB_matrix.entry_id 1D79 _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 1D79 _atom_sites.fract_transf_matrix[1][1] 0.030921 _atom_sites.fract_transf_matrix[1][2] 0.017852 _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] 0.035605 _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] 0.012740 _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 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 DG 1 1 1 DG G A . n A 1 2 DT 2 2 2 DT T A . n A 1 3 DG 3 3 3 DG G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DC 6 6 6 DC C A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C 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 9 9 HOH HOH A . B 2 HOH 2 10 10 HOH HOH A . B 2 HOH 3 11 11 HOH HOH A . B 2 HOH 4 12 12 HOH HOH A . B 2 HOH 5 13 13 HOH HOH A . B 2 HOH 6 14 14 HOH HOH A . B 2 HOH 7 15 15 HOH HOH A . B 2 HOH 8 16 16 HOH HOH A . B 2 HOH 9 17 17 HOH HOH A . B 2 HOH 10 18 18 HOH HOH A . B 2 HOH 11 19 19 HOH HOH A . B 2 HOH 12 20 20 HOH HOH A . B 2 HOH 13 21 21 HOH HOH A . B 2 HOH 14 22 22 HOH HOH A . B 2 HOH 15 23 23 HOH HOH A . B 2 HOH 16 24 24 HOH HOH A . B 2 HOH 17 25 25 HOH HOH A . B 2 HOH 18 26 26 HOH HOH A . B 2 HOH 19 27 27 HOH HOH A . B 2 HOH 20 28 28 HOH HOH A . B 2 HOH 21 29 29 HOH HOH A . B 2 HOH 22 30 30 HOH HOH A . B 2 HOH 23 31 31 HOH HOH A . B 2 HOH 24 32 32 HOH HOH A . B 2 HOH 25 33 33 HOH HOH A . B 2 HOH 26 34 34 HOH HOH A . B 2 HOH 27 35 35 HOH HOH A . B 2 HOH 28 36 36 HOH HOH A . B 2 HOH 29 37 37 HOH HOH A . B 2 HOH 30 38 38 HOH HOH A . B 2 HOH 31 39 39 HOH HOH A . B 2 HOH 32 40 40 HOH HOH A . B 2 HOH 33 41 41 HOH HOH A . B 2 HOH 34 42 42 HOH HOH A . B 2 HOH 35 43 43 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' 12_555 x,x-y,-z+1/6 0.4986097458 0.8652107365 0.0000000000 0.0000000000 0.8684454431 -0.4986097458 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 13.0821559393 # 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' 1 3 2023-03-22 # _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' 'Structure summary' # 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' audit_author 2 4 'Structure model' citation_author 3 4 'Structure model' database_2 # 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' '_audit_author.name' 2 4 'Structure model' '_citation_author.name' 3 4 'Structure model' '_database_2.pdbx_DOI' 4 4 'Structure model' '_database_2.pdbx_database_accession' # 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 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 WATERS' fix 'X-RAY DIFFRACTION' # _software.name NUCLSQ _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 _software.date ? _software.type ? _software.location ? _software.language ? # 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 DG 3 ? ? "O5'" A DG 3 ? ? 1.660 1.593 0.067 0.010 N 2 1 "O3'" A DG 3 ? ? P A DT 4 ? ? 1.517 1.607 -0.090 0.012 Y 3 1 P A DT 4 ? ? "O5'" A DT 4 ? ? 1.661 1.593 0.068 0.010 N 4 1 P A DC 8 ? ? "O5'" A DC 8 ? ? 1.667 1.593 0.074 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 "O5'" A DT 2 ? ? P A DT 2 ? ? OP2 A DT 2 ? ? 118.07 110.70 7.37 1.20 N 2 1 "O5'" A DT 2 ? ? "C5'" A DT 2 ? ? "C4'" A DT 2 ? ? 104.05 109.40 -5.35 0.80 N 3 1 C2 A DT 2 ? ? N3 A DT 2 ? ? C4 A DT 2 ? ? 123.03 127.20 -4.17 0.60 N 4 1 N3 A DT 2 ? ? C4 A DT 2 ? ? C5 A DT 2 ? ? 120.37 115.20 5.17 0.60 N 5 1 "O3'" A DT 2 ? ? P A DG 3 ? ? OP2 A DG 3 ? ? 121.21 110.50 10.71 1.10 Y 6 1 "O5'" A DG 3 ? ? P A DG 3 ? ? OP2 A DG 3 ? ? 98.31 105.70 -7.39 0.90 N 7 1 "O5'" A DG 3 ? ? "C5'" A DG 3 ? ? "C4'" A DG 3 ? ? 104.44 109.40 -4.96 0.80 N 8 1 "O3'" A DG 3 ? ? P A DT 4 ? ? OP2 A DT 4 ? ? 117.59 110.50 7.09 1.10 Y 9 1 "O4'" A DT 4 ? ? "C1'" A DT 4 ? ? N1 A DT 4 ? ? 110.76 108.30 2.46 0.30 N 10 1 C2 A DT 4 ? ? N3 A DT 4 ? ? C4 A DT 4 ? ? 122.71 127.20 -4.49 0.60 N 11 1 OP1 A DA 5 ? ? P A DA 5 ? ? OP2 A DA 5 ? ? 110.14 119.60 -9.46 1.50 N 12 1 C6 A DA 5 ? ? N1 A DA 5 ? ? C2 A DA 5 ? ? 122.83 118.60 4.23 0.60 N 13 1 N1 A DA 5 ? ? C2 A DA 5 ? ? N3 A DA 5 ? ? 123.39 129.30 -5.91 0.50 N 14 1 C2 A DA 5 ? ? N3 A DA 5 ? ? C4 A DA 5 ? ? 114.02 110.60 3.42 0.50 N 15 1 N3 A DC 6 ? ? C4 A DC 6 ? ? C5 A DC 6 ? ? 119.26 121.90 -2.64 0.40 N 16 1 C6 A DA 7 ? ? N1 A DA 7 ? ? C2 A DA 7 ? ? 122.65 118.60 4.05 0.60 N 17 1 N1 A DA 7 ? ? C2 A DA 7 ? ? N3 A DA 7 ? ? 125.51 129.30 -3.79 0.50 N 18 1 C5 A DA 7 ? ? C6 A DA 7 ? ? N1 A DA 7 ? ? 114.09 117.70 -3.61 0.50 N 19 1 "O5'" A DC 8 ? ? "C5'" A DC 8 ? ? "C4'" A DC 8 ? ? 103.51 109.40 -5.89 0.80 N 20 1 N3 A DC 8 ? ? C4 A DC 8 ? ? C5 A DC 8 ? ? 119.39 121.90 -2.51 0.40 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1D79 'double helix' 1D79 'a-form double helix' # 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 DG 1 1_555 A DC 8 12_555 -0.303 -0.179 -0.233 -14.935 -19.194 -0.365 1 A_DG1:DC8_A A 1 ? A 8 ? 19 1 1 A DT 2 1_555 A DA 7 12_555 -0.004 -0.125 -0.071 -18.067 -8.707 -3.144 2 A_DT2:DA7_A A 2 ? A 7 ? 20 1 1 A DG 3 1_555 A DC 6 12_555 -0.163 -0.166 0.032 -8.232 -13.305 0.751 3 A_DG3:DC6_A A 3 ? A 6 ? 19 1 1 A DT 4 1_555 A DA 5 12_555 0.005 -0.223 0.167 -1.880 -12.140 -2.352 4 A_DT4:DA5_A A 4 ? A 5 ? 20 1 1 A DA 5 1_555 A DT 4 12_555 -0.010 -0.219 0.167 1.888 -12.144 -2.319 5 A_DA5:DT4_A A 5 ? A 4 ? 20 1 1 A DC 6 1_555 A DG 3 12_555 0.161 -0.157 0.032 8.219 -13.310 0.779 6 A_DC6:DG3_A A 6 ? A 3 ? 19 1 1 A DA 7 1_555 A DT 2 12_555 0.008 -0.120 -0.070 18.026 -8.691 -3.126 7 A_DA7:DT2_A A 7 ? A 2 ? 20 1 1 A DC 8 1_555 A DG 1 12_555 0.308 -0.179 -0.232 14.908 -19.151 -0.345 8 A_DC8:DG1_A A 8 ? A 1 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 A DC 8 12_555 A DT 2 1_555 A DA 7 12_555 -0.644 -1.347 3.394 1.737 -1.361 36.131 -1.969 1.291 3.407 -2.191 -2.797 36.196 1 AA_DG1DT2:DA7DC8_AA A 1 ? A 8 ? A 2 ? A 7 ? 1 A DT 2 1_555 A DA 7 12_555 A DG 3 1_555 A DC 6 12_555 0.690 -0.986 3.150 -2.030 12.887 28.752 -3.968 -1.610 2.442 24.426 3.847 31.517 2 AA_DT2DG3:DC6DA7_AA A 2 ? A 7 ? A 3 ? A 6 ? 1 A DG 3 1_555 A DC 6 12_555 A DT 4 1_555 A DA 5 12_555 -0.583 -1.150 3.177 -1.660 5.947 32.847 -2.930 0.754 2.954 10.402 2.904 33.406 3 AA_DG3DT4:DA5DC6_AA A 3 ? A 6 ? A 4 ? A 5 ? 1 A DT 4 1_555 A DA 5 12_555 A DA 5 1_555 A DT 4 12_555 -0.002 -1.138 3.112 -0.005 13.059 30.901 -3.882 0.002 2.445 23.250 0.009 33.485 4 AA_DT4DA5:DT4DA5_AA A 4 ? A 5 ? A 5 ? A 4 ? 1 A DA 5 1_555 A DT 4 12_555 A DC 6 1_555 A DG 3 12_555 0.575 -1.147 3.176 1.655 5.949 32.827 -2.929 -0.742 2.953 10.411 -2.897 33.387 5 AA_DA5DC6:DG3DT4_AA A 5 ? A 4 ? A 6 ? A 3 ? 1 A DC 6 1_555 A DG 3 12_555 A DA 7 1_555 A DT 2 12_555 -0.695 -0.982 3.148 2.027 12.888 28.749 -3.961 1.619 2.441 24.430 -3.842 31.514 6 AA_DC6DA7:DT2DG3_AA A 6 ? A 3 ? A 7 ? A 2 ? 1 A DA 7 1_555 A DT 2 12_555 A DC 8 1_555 A DG 1 12_555 0.643 -1.339 3.391 -1.737 -1.360 36.129 -1.957 -1.288 3.404 -2.190 2.798 36.194 7 AA_DA7DC8:DG1DT2_AA A 7 ? A 2 ? A 8 ? A 1 ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #