data_3DNB # _entry.id 3DNB # _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 3DNB pdb_00003dnb 10.2210/pdb3dnb/pdb RCSB BDJ008 ? ? WWPDB D_1000178941 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3DNB _pdbx_database_status.recvd_initial_deposition_date 1988-03-18 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site BNL _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 'Prive, G.G.' 1 'Dickerson, R.E.' 2 # 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-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 1991 JMOBAK UK 0022-2836 0070 ? 1988677 '10.1016/0022-2836(91)90619-H' 1 'Helix Geometry, Hydration, and G.A Mismatch in a B-DNA Decamer' Science 238 498 504 1987 SCIEAS US 0036-8075 0038 ? ? ? 2 'A Mismatch Decamer as a Model for General-Sequence B-DNA' 'Structure and Expression' 2 27 47 1988 ? ? 0-940030-22-5 0837 'Adenine Press, Albany, NY' ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Prive, G.G.' 1 ? primary 'Yanagi, K.' 2 ? primary 'Dickerson, R.E.' 3 ? 1 'Prive, G.G.' 4 ? 1 'Heinemann, U.' 5 ? 1 'Chandrasegaran, S.' 6 ? 1 'Kan, L.S.' 7 ? 1 'Kopka, M.L.' 8 ? 1 'Dickerson, R.E.' 9 ? 2 'Prive, G.G.' 10 ? 2 'Heinemann, U.' 11 ? 2 'Chandrasegaran, S.' 12 ? 2 'Kan, L.-S.' 13 ? 2 'Kopka, M.L.' 14 ? 2 'Dickerson, R.E.' 15 ? # _cell.entry_id 3DNB _cell.length_a 32.520 _cell.length_b 26.170 _cell.length_c 34.300 _cell.angle_alpha 90.00 _cell.angle_beta 118.90 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DNB _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*GP*AP*TP*TP*GP*G)-3') ; 3069.030 1 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 3 ? ? ? ? 3 water nat water 18.015 69 ? ? ? ? # _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)(DG)(DA)(DT)(DT)(DG)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CCAAGATTGG _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 DG 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 3DNB _struct_ref.pdbx_db_accession 3DNB _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 3DNB _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 3DNB _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 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # _exptl.entry_id 3DNB _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 38.45 _exptl_crystal.density_Matthews 2.00 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'VAPOR DIFFUSION, 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 MGCL2 ? ? ? 1 4 2 WATER ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details 'ROOM TEMPERATURE' _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'NICOLET P1' _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 ? _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 3DNB _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 8.000 _reflns.d_resolution_high 1.300 _reflns.number_obs ? _reflns.number_all ? _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 3DNB _refine.ls_number_reflns_obs 4016 _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 0.1640000 _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 0.53 _refine.occupancy_max 1.00 _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.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _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_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 204 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 69 _refine_hist.number_atoms_total 276 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low 8.000 # 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 0.019 ? ? ? '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 ? ? ? ? 'X-RAY DIFFRACTION' ? n_sugar_bond_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? n_phos_bond_d ? ? ? ? '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 3DNB _struct.title 'HELIX GEOMETRY, HYDRATION, AND G.A MISMATCH IN A B-DNA DECAMER' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DNB _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, MISMATCHED, 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 2 ? D N N 2 ? E N N 3 ? # _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 ? ? A DA 6 OP2 ? ? ? 1_555 B MG . MG ? ? A DA 6 A MG 11 1_555 ? ? ? ? ? ? ? 2.009 ? ? metalc2 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 11 A HOH 14 1_555 ? ? ? ? ? ? ? 2.003 ? ? metalc3 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 11 A HOH 15 1_555 ? ? ? ? ? ? ? 2.036 ? ? metalc4 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 11 A HOH 16 1_555 ? ? ? ? ? ? ? 2.013 ? ? metalc5 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 11 A HOH 17 1_555 ? ? ? ? ? ? ? 1.997 ? ? metalc6 metalc ? ? B MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 11 A HOH 18 1_555 ? ? ? ? ? ? ? 2.021 ? ? metalc7 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 12 A HOH 19 1_555 ? ? ? ? ? ? ? 2.002 ? ? metalc8 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 12 A HOH 20 1_555 ? ? ? ? ? ? ? 2.005 ? ? metalc9 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 12 A HOH 21 1_555 ? ? ? ? ? ? ? 2.016 ? ? metalc10 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 12 A HOH 22 1_555 ? ? ? ? ? ? ? 2.015 ? ? metalc11 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 12 A HOH 23 1_555 ? ? ? ? ? ? ? 1.995 ? ? metalc12 metalc ? ? C MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 12 A HOH 24 1_555 ? ? ? ? ? ? ? 2.014 ? ? metalc13 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 A HOH 25 1_555 ? ? ? ? ? ? ? 1.997 ? ? metalc14 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 A HOH 26 1_555 ? ? ? ? ? ? ? 2.012 ? ? metalc15 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 A HOH 27 1_555 ? ? ? ? ? ? ? 2.020 ? ? metalc16 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 A HOH 28 1_555 ? ? ? ? ? ? ? 2.003 ? ? metalc17 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 A HOH 29 1_555 ? ? ? ? ? ? ? 2.013 ? ? metalc18 metalc ? ? D MG . MG ? ? ? 1_555 E HOH . O ? ? A MG 13 A HOH 30 1_555 ? ? ? ? ? ? ? 1.983 ? ? 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 DG 5 N1 ? ? ? 1_555 A DA 6 N1 ? ? A DG 5 A DA 6 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog12 hydrog ? ? A DG 5 O6 ? ? ? 1_555 A DA 6 N6 ? ? A DG 5 A DA 6 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog13 hydrog ? ? A DA 6 N1 ? ? ? 1_555 A DG 5 N1 ? ? A DA 6 A DG 5 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog14 hydrog ? ? A DA 6 N6 ? ? ? 1_555 A DG 5 O6 ? ? A DA 6 A DG 5 2_555 ? ? ? ? ? ? TYPE_8_PAIR ? ? ? hydrog15 hydrog ? ? A DT 7 N3 ? ? ? 1_555 A DA 4 N1 ? ? A DT 7 A DA 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DT 7 O4 ? ? ? 1_555 A DA 4 N6 ? ? A DT 7 A DA 4 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 8 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 8 A DA 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 8 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 8 A DA 3 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 2 N3 ? ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 2 O2 ? ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 2 N4 ? ? A DG 9 A DC 2 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 10 N1 ? ? ? 1_555 A DC 1 N3 ? ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 10 N2 ? ? ? 1_555 A DC 1 O2 ? ? A DG 10 A DC 1 2_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 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 MG 11 ? 6 'BINDING SITE FOR RESIDUE MG A 11' AC2 Software A MG 12 ? 6 'BINDING SITE FOR RESIDUE MG A 12' AC3 Software A MG 13 ? 6 'BINDING SITE FOR RESIDUE MG A 13' # 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 6 DA A 6 ? DA A 6 . ? 1_555 ? 2 AC1 6 HOH E . ? HOH A 14 . ? 1_555 ? 3 AC1 6 HOH E . ? HOH A 15 . ? 1_555 ? 4 AC1 6 HOH E . ? HOH A 16 . ? 1_555 ? 5 AC1 6 HOH E . ? HOH A 17 . ? 1_555 ? 6 AC1 6 HOH E . ? HOH A 18 . ? 1_555 ? 7 AC2 6 HOH E . ? HOH A 19 . ? 1_555 ? 8 AC2 6 HOH E . ? HOH A 20 . ? 1_555 ? 9 AC2 6 HOH E . ? HOH A 21 . ? 1_555 ? 10 AC2 6 HOH E . ? HOH A 22 . ? 1_555 ? 11 AC2 6 HOH E . ? HOH A 23 . ? 1_555 ? 12 AC2 6 HOH E . ? HOH A 24 . ? 1_555 ? 13 AC3 6 HOH E . ? HOH A 25 . ? 1_555 ? 14 AC3 6 HOH E . ? HOH A 26 . ? 1_555 ? 15 AC3 6 HOH E . ? HOH A 27 . ? 1_555 ? 16 AC3 6 HOH E . ? HOH A 28 . ? 1_555 ? 17 AC3 6 HOH E . ? HOH A 29 . ? 1_555 ? 18 AC3 6 HOH E . ? HOH A 30 . ? 1_555 ? # _database_PDB_matrix.entry_id 3DNB _database_PDB_matrix.origx[1][1] 0.875465 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.483282 _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] -0.483282 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 0.875465 _database_PDB_matrix.origx_vector[3] 0.000000 # _atom_sites.entry_id 3DNB _atom_sites.fract_transf_matrix[1][1] 0.030750 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.016975 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.038212 _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] 0.033302 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C MG 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 DG 5 5 5 DG G 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 MG 1 11 11 MG MG A . C 2 MG 1 12 12 MG MG A . D 2 MG 1 13 13 MG MG A . E 3 HOH 1 14 14 HOH HOH A . E 3 HOH 2 15 15 HOH HOH A . E 3 HOH 3 16 16 HOH HOH A . E 3 HOH 4 17 17 HOH HOH A . E 3 HOH 5 18 18 HOH HOH A . E 3 HOH 6 19 19 HOH HOH A . E 3 HOH 7 20 20 HOH HOH A . E 3 HOH 8 21 21 HOH HOH A . E 3 HOH 9 22 22 HOH HOH A . E 3 HOH 10 23 23 HOH HOH A . E 3 HOH 11 24 24 HOH HOH A . E 3 HOH 12 25 25 HOH HOH A . E 3 HOH 13 26 26 HOH HOH A . E 3 HOH 14 27 27 HOH HOH A . E 3 HOH 15 28 28 HOH HOH A . E 3 HOH 16 29 29 HOH HOH A . E 3 HOH 17 30 30 HOH HOH A . E 3 HOH 18 31 31 HOH HOH A . E 3 HOH 19 32 32 HOH HOH A . E 3 HOH 20 33 33 HOH HOH A . E 3 HOH 21 34 34 HOH HOH A . E 3 HOH 22 35 35 HOH HOH A . E 3 HOH 23 36 36 HOH HOH A . E 3 HOH 24 37 37 HOH HOH A . E 3 HOH 25 38 38 HOH HOH A . E 3 HOH 26 39 39 HOH HOH A . E 3 HOH 27 40 40 HOH HOH A . E 3 HOH 28 41 41 HOH HOH A . E 3 HOH 29 42 42 HOH HOH A . E 3 HOH 30 43 43 HOH HOH A . E 3 HOH 31 44 44 HOH HOH A . E 3 HOH 32 45 45 HOH HOH A . E 3 HOH 33 46 46 HOH HOH A . E 3 HOH 34 47 47 HOH HOH A . E 3 HOH 35 48 48 HOH HOH A . E 3 HOH 36 49 49 HOH HOH A . E 3 HOH 37 50 50 HOH HOH A . E 3 HOH 38 51 51 HOH HOH A . E 3 HOH 39 52 52 HOH HOH A . E 3 HOH 40 53 53 HOH HOH A . E 3 HOH 41 54 54 HOH HOH A . E 3 HOH 42 55 55 HOH HOH A . E 3 HOH 43 56 56 HOH HOH A . E 3 HOH 44 57 57 HOH HOH A . E 3 HOH 45 58 58 HOH HOH A . E 3 HOH 46 59 59 HOH HOH A . E 3 HOH 47 60 60 HOH HOH A . E 3 HOH 48 61 61 HOH HOH A . E 3 HOH 49 62 62 HOH HOH A . E 3 HOH 50 63 63 HOH HOH A . E 3 HOH 51 64 64 HOH HOH A . E 3 HOH 52 65 65 HOH HOH A . E 3 HOH 53 66 66 HOH HOH A . E 3 HOH 54 67 67 HOH HOH A . E 3 HOH 55 68 68 HOH HOH A . E 3 HOH 56 69 69 HOH HOH A . E 3 HOH 57 70 70 HOH HOH A . E 3 HOH 58 71 71 HOH HOH A . E 3 HOH 59 72 72 HOH HOH A . E 3 HOH 60 73 73 HOH HOH A . E 3 HOH 61 74 74 HOH HOH A . E 3 HOH 62 75 75 HOH HOH A . E 3 HOH 63 76 76 HOH HOH A . E 3 HOH 64 77 77 HOH HOH A . E 3 HOH 65 78 78 HOH HOH A . E 3 HOH 66 79 79 HOH HOH A . E 3 HOH 67 80 80 HOH HOH A . E 3 HOH 68 81 81 HOH HOH A . E 3 HOH 69 82 82 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,C,D,E # 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_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 OP2 ? A DA 6 ? A DA 6 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 14 ? 1_555 102.0 ? 2 OP2 ? A DA 6 ? A DA 6 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 15 ? 1_555 82.0 ? 3 O ? E HOH . ? A HOH 14 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 15 ? 1_555 176.0 ? 4 OP2 ? A DA 6 ? A DA 6 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 16 ? 1_555 98.1 ? 5 O ? E HOH . ? A HOH 14 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 16 ? 1_555 89.1 ? 6 O ? E HOH . ? A HOH 15 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 16 ? 1_555 89.9 ? 7 OP2 ? A DA 6 ? A DA 6 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 17 ? 1_555 83.0 ? 8 O ? E HOH . ? A HOH 14 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 17 ? 1_555 90.9 ? 9 O ? E HOH . ? A HOH 15 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 17 ? 1_555 89.9 ? 10 O ? E HOH . ? A HOH 16 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 17 ? 1_555 178.9 ? 11 OP2 ? A DA 6 ? A DA 6 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 18 ? 1_555 166.6 ? 12 O ? E HOH . ? A HOH 14 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 18 ? 1_555 89.1 ? 13 O ? E HOH . ? A HOH 15 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 18 ? 1_555 87.0 ? 14 O ? E HOH . ? A HOH 16 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 18 ? 1_555 89.6 ? 15 O ? E HOH . ? A HOH 17 ? 1_555 MG ? B MG . ? A MG 11 ? 1_555 O ? E HOH . ? A HOH 18 ? 1_555 89.3 ? 16 O ? E HOH . ? A HOH 19 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 20 ? 1_555 179.0 ? 17 O ? E HOH . ? A HOH 19 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 21 ? 1_555 89.9 ? 18 O ? E HOH . ? A HOH 20 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 21 ? 1_555 90.5 ? 19 O ? E HOH . ? A HOH 19 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 22 ? 1_555 89.5 ? 20 O ? E HOH . ? A HOH 20 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 22 ? 1_555 90.0 ? 21 O ? E HOH . ? A HOH 21 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 22 ? 1_555 178.3 ? 22 O ? E HOH . ? A HOH 19 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 23 ? 1_555 90.4 ? 23 O ? E HOH . ? A HOH 20 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 23 ? 1_555 90.4 ? 24 O ? E HOH . ? A HOH 21 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 23 ? 1_555 92.0 ? 25 O ? E HOH . ? A HOH 22 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 23 ? 1_555 89.7 ? 26 O ? E HOH . ? A HOH 19 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 24 ? 1_555 89.7 ? 27 O ? E HOH . ? A HOH 20 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 24 ? 1_555 89.5 ? 28 O ? E HOH . ? A HOH 21 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 24 ? 1_555 89.3 ? 29 O ? E HOH . ? A HOH 22 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 24 ? 1_555 89.1 ? 30 O ? E HOH . ? A HOH 23 ? 1_555 MG ? C MG . ? A MG 12 ? 1_555 O ? E HOH . ? A HOH 24 ? 1_555 178.8 ? 31 O ? E HOH . ? A HOH 25 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 26 ? 1_555 179.2 ? 32 O ? E HOH . ? A HOH 25 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 27 ? 1_555 90.0 ? 33 O ? E HOH . ? A HOH 26 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 27 ? 1_555 89.3 ? 34 O ? E HOH . ? A HOH 25 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 88.4 ? 35 O ? E HOH . ? A HOH 26 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 92.2 ? 36 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 28 ? 1_555 176.3 ? 37 O ? E HOH . ? A HOH 25 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 90.4 ? 38 O ? E HOH . ? A HOH 26 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 89.1 ? 39 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 88.3 ? 40 O ? E HOH . ? A HOH 28 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 29 ? 1_555 88.3 ? 41 O ? E HOH . ? A HOH 25 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 30 ? 1_555 89.2 ? 42 O ? E HOH . ? A HOH 26 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 30 ? 1_555 91.3 ? 43 O ? E HOH . ? A HOH 27 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 30 ? 1_555 89.6 ? 44 O ? E HOH . ? A HOH 28 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 30 ? 1_555 93.7 ? 45 O ? E HOH . ? A HOH 29 ? 1_555 MG ? D MG . ? A MG 13 ? 1_555 O ? E HOH . ? A HOH 30 ? 1_555 177.9 ? # 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 1989-01-09 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_conn_angle 7 4 'Structure model' pdbx_validate_rmsd_angle 8 4 'Structure model' pdbx_validate_rmsd_bond 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_sites.fract_transf_matrix[1][1]' 4 4 'Structure model' '_atom_sites.fract_transf_matrix[1][3]' 5 4 'Structure model' '_atom_sites.fract_transf_matrix[3][1]' 6 4 'Structure model' '_atom_sites.fract_transf_matrix[3][3]' 7 4 'Structure model' '_database_2.pdbx_DOI' 8 4 'Structure model' '_database_2.pdbx_database_accession' 9 4 'Structure model' '_database_PDB_matrix.origx[1][1]' 10 4 'Structure model' '_database_PDB_matrix.origx[1][3]' 11 4 'Structure model' '_database_PDB_matrix.origx[3][1]' 12 4 'Structure model' '_database_PDB_matrix.origx[3][3]' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 17 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 18 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 19 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 20 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 21 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 22 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 23 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 24 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 25 4 'Structure model' '_pdbx_struct_conn_angle.value' 26 4 'Structure model' '_pdbx_validate_rmsd_angle.angle_deviation' 27 4 'Structure model' '_pdbx_validate_rmsd_angle.angle_value' 28 4 'Structure model' '_pdbx_validate_rmsd_bond.bond_deviation' 29 4 'Structure model' '_pdbx_validate_rmsd_bond.bond_value' 30 4 'Structure model' '_struct_conn.pdbx_dist_value' 31 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 32 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 33 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 34 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 35 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 36 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 37 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 38 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 39 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 40 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 41 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 42 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 43 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 44 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 45 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 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' ref 'X-RAY DIFFRACTION' # _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 C4 A DC 1 ? ? C5 A DC 1 ? ? 1.475 1.425 0.050 0.008 N 2 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? 1.490 1.420 0.070 0.011 N 3 1 "O4'" A DA 3 ? ? "C4'" A DA 3 ? ? 1.382 1.446 -0.064 0.010 N 4 1 "C2'" A DT 7 ? ? "C1'" A DT 7 ? ? 1.445 1.518 -0.073 0.010 N 5 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? 1.506 1.420 0.086 0.011 N 6 1 "O4'" A DT 8 ? ? "C1'" A DT 8 ? ? 1.496 1.420 0.076 0.011 N 7 1 C4 A DT 8 ? ? O4 A DT 8 ? ? 1.290 1.228 0.062 0.009 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 C2 A DC 1 ? ? N3 A DC 1 ? ? C4 A DC 1 ? ? 124.01 119.90 4.11 0.50 N 2 1 N3 A DC 1 ? ? C4 A DC 1 ? ? C5 A DC 1 ? ? 118.44 121.90 -3.46 0.40 N 3 1 N3 A DC 1 ? ? C4 A DC 1 ? ? N4 A DC 1 ? ? 122.90 118.00 4.90 0.70 N 4 1 C6 A DC 2 ? ? N1 A DC 2 ? ? C2 A DC 2 ? ? 117.05 120.30 -3.25 0.40 N 5 1 N3 A DC 2 ? ? C4 A DC 2 ? ? C5 A DC 2 ? ? 117.54 121.90 -4.36 0.40 N 6 1 "O4'" A DA 3 ? ? "C1'" A DA 3 ? ? N9 A DA 3 ? ? 103.04 108.00 -4.96 0.70 N 7 1 N1 A DA 3 ? ? C2 A DA 3 ? ? N3 A DA 3 ? ? 124.68 129.30 -4.62 0.50 N 8 1 "O5'" A DA 4 ? ? "C5'" A DA 4 ? ? "C4'" A DA 4 ? ? 104.16 109.40 -5.24 0.80 N 9 1 C6 A DA 4 ? ? N1 A DA 4 ? ? C2 A DA 4 ? ? 122.38 118.60 3.78 0.60 N 10 1 N1 A DA 4 ? ? C2 A DA 4 ? ? N3 A DA 4 ? ? 123.16 129.30 -6.14 0.50 N 11 1 "O5'" A DG 5 ? ? "C5'" A DG 5 ? ? "C4'" A DG 5 ? ? 104.25 109.40 -5.15 0.80 N 12 1 "C3'" A DG 5 ? ? "C2'" A DG 5 ? ? "C1'" A DG 5 ? ? 97.46 102.40 -4.94 0.80 N 13 1 "O4'" A DG 5 ? ? "C1'" A DG 5 ? ? N9 A DG 5 ? ? 114.68 108.30 6.38 0.30 N 14 1 C5 A DG 5 ? ? C6 A DG 5 ? ? N1 A DG 5 ? ? 114.56 111.50 3.06 0.50 N 15 1 C6 A DA 6 ? ? N1 A DA 6 ? ? C2 A DA 6 ? ? 122.72 118.60 4.12 0.60 N 16 1 C5 A DA 6 ? ? C6 A DA 6 ? ? N1 A DA 6 ? ? 113.44 117.70 -4.26 0.50 N 17 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 103.71 108.00 -4.29 0.70 N 18 1 N1 A DT 7 ? ? C2 A DT 7 ? ? N3 A DT 7 ? ? 119.29 114.60 4.69 0.60 N 19 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 121.34 127.20 -5.86 0.60 N 20 1 N3 A DT 7 ? ? C4 A DT 7 ? ? C5 A DT 7 ? ? 119.20 115.20 4.00 0.60 N 21 1 N1 A DT 8 ? ? C2 A DT 8 ? ? N3 A DT 8 ? ? 120.44 114.60 5.84 0.60 N 22 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 119.65 127.20 -7.55 0.60 N 23 1 N3 A DT 8 ? ? C4 A DT 8 ? ? C5 A DT 8 ? ? 120.86 115.20 5.66 0.60 N 24 1 N3 A DT 8 ? ? C4 A DT 8 ? ? O4 A DT 8 ? ? 114.75 119.90 -5.15 0.60 N 25 1 OP1 A DG 9 ? ? P A DG 9 ? ? OP2 A DG 9 ? ? 108.99 119.60 -10.61 1.50 N 26 1 "O4'" A DG 9 ? ? "C1'" A DG 9 ? ? N9 A DG 9 ? ? 102.78 108.00 -5.22 0.70 N 27 1 C6 A DG 9 ? ? N1 A DG 9 ? ? C2 A DG 9 ? ? 121.41 125.10 -3.69 0.60 N 28 1 C5 A DG 9 ? ? C6 A DG 9 ? ? N1 A DG 9 ? ? 115.38 111.50 3.88 0.50 N 29 1 C6 A DG 10 ? ? N1 A DG 10 ? ? C2 A DG 10 ? ? 121.20 125.10 -3.90 0.60 N 30 1 C5 A DG 10 ? ? C6 A DG 10 ? ? N1 A DG 10 ? ? 116.19 111.50 4.69 0.50 N # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 3DNB 'b-form double helix' 3DNB 'mismatched base pair' # 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 0.115 -0.154 0.214 -7.984 -12.404 -2.174 1 A_DC1:DG10_A A 1 ? A 10 ? 19 1 1 A DC 2 1_555 A DG 9 2_555 0.290 -0.162 0.108 1.217 -8.719 -1.701 2 A_DC2:DG9_A A 2 ? A 9 ? 19 1 1 A DA 3 1_555 A DT 8 2_555 0.119 -0.033 0.090 1.112 -9.304 1.621 3 A_DA3:DT8_A A 3 ? A 8 ? 20 1 1 A DA 4 1_555 A DT 7 2_555 0.117 -0.024 -0.071 5.547 -17.667 0.540 4 A_DA4:DT7_A A 4 ? A 7 ? 20 1 1 A DG 5 1_555 A DA 6 2_555 -0.003 1.409 -0.524 5.304 -24.046 -11.226 5 A_DG5:DA6_A A 5 ? A 6 ? 8 ? 1 A DA 6 1_555 A DG 5 2_555 0.003 1.409 -0.524 -5.304 -24.046 -11.226 6 A_DA6:DG5_A A 6 ? A 5 ? 8 ? 1 A DT 7 1_555 A DA 4 2_555 -0.117 -0.024 -0.071 -5.547 -17.667 0.540 7 A_DT7:DA4_A A 7 ? A 4 ? 20 1 1 A DT 8 1_555 A DA 3 2_555 -0.119 -0.033 0.090 -1.112 -9.304 1.621 8 A_DT8:DA3_A A 8 ? A 3 ? 20 1 1 A DG 9 1_555 A DC 2 2_555 -0.290 -0.162 0.108 -1.218 -8.719 -1.701 9 A_DG9:DC2_A A 9 ? A 2 ? 19 1 1 A DG 10 1_555 A DC 1 2_555 -0.115 -0.154 0.214 7.984 -12.404 -2.174 10 A_DG10:DC1_A A 10 ? 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 DC 1 1_555 A DG 10 2_555 A DC 2 1_555 A DG 9 2_555 -0.399 0.237 3.167 1.497 4.893 29.269 -0.536 1.084 3.141 9.591 -2.934 29.703 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 0.184 2.769 3.358 1.842 -8.234 49.307 3.853 -0.089 2.894 -9.786 -2.189 49.980 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 0.356 0.835 3.433 -1.431 14.984 25.350 -1.955 -1.044 3.368 30.913 2.952 29.419 3 AA_DA3DA4:DT7DT8_AA A 3 ? A 8 ? A 4 ? A 7 ? 1 A DA 4 1_555 A DT 7 2_555 A DG 5 1_555 A DA 6 2_555 -1.211 0.267 3.192 1.043 -0.628 33.479 0.564 2.267 3.149 -1.089 -1.810 33.500 4 AA_DA4DG5:DA6DT7_AA A 4 ? A 7 ? A 5 ? A 6 ? 1 A DG 5 1_555 A DA 6 2_555 A DA 6 1_555 A DG 5 2_555 0.000 1.478 3.326 0.000 -2.380 42.547 2.275 0.000 3.243 -3.276 0.000 42.611 5 AA_DG5DA6:DG5DA6_AA A 5 ? A 6 ? A 6 ? A 5 ? 1 A DA 6 1_555 A DG 5 2_555 A DT 7 1_555 A DA 4 2_555 1.211 0.267 3.192 -1.043 -0.628 33.479 0.564 -2.267 3.149 -1.089 1.810 33.500 6 AA_DA6DT7:DA4DG5_AA A 6 ? A 5 ? A 7 ? A 4 ? 1 A DT 7 1_555 A DA 4 2_555 A DT 8 1_555 A DA 3 2_555 -0.356 0.835 3.433 1.431 14.984 25.350 -1.955 1.044 3.368 30.913 -2.952 29.419 7 AA_DT7DT8:DA3DA4_AA A 7 ? A 4 ? A 8 ? A 3 ? 1 A DT 8 1_555 A DA 3 2_555 A DG 9 1_555 A DC 2 2_555 -0.184 2.769 3.358 -1.842 -8.234 49.307 3.853 0.089 2.894 -9.786 2.189 49.980 8 AA_DT8DG9:DC2DA3_AA A 8 ? A 3 ? A 9 ? A 2 ? 1 A DG 9 1_555 A DC 2 2_555 A DG 10 1_555 A DC 1 2_555 0.399 0.237 3.167 -1.497 4.893 29.269 -0.536 -1.084 3.141 9.591 2.934 29.703 9 AA_DG9DG10:DC1DC2_AA A 9 ? A 2 ? A 10 ? A 1 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'MAGNESIUM ION' MG 3 water HOH #