data_8OE9 # _entry.id 8OE9 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.388 _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 8OE9 pdb_00008oe9 10.2210/pdb8oe9/pdb WWPDB D_1292129077 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2024-03-27 # _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 ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8OE9 _pdbx_database_status.recvd_initial_deposition_date 2023-03-10 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_contact_author.id 2 _pdbx_contact_author.email james.hall@reading.ac.uk _pdbx_contact_author.name_first James _pdbx_contact_author.name_last Hall _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-3716-4378 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Lambert, M.C.' 1 0000-0002-2860-8689 'Hall, J.P.' 2 0000-0003-3716-4378 # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country ? _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'To Be Published' _citation.journal_id_ASTM ? _citation.journal_id_CSD 0353 _citation.journal_id_ISSN ? _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title ;Structural analysis of peroxide-soaked DNA crystals containing ordered copper binding sites: towards understanding oxidative damage at the atomic scale ; _citation.year ? _citation.database_id_CSD ? _citation.pdbx_database_id_DOI ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Lambert, M.C.' 1 0000-0002-2860-8689 primary 'Hall, J.P.' 2 0000-0003-3716-4378 # 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*GP*CP*GP*CP*G)-3') ; 1810.205 2 ? ? ? ? 2 non-polymer syn SPERMINE 202.340 1 ? ? ? ? 3 water nat water 18.015 94 ? ? ? ? # _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)(DG)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 SPERMINE SPM 3 water HOH # 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 DG n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 6 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # 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 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 HOH non-polymer . WATER ? 'H2 O' 18.015 SPM non-polymer . SPERMINE ? 'C10 H26 N4' 202.340 # 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 DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DG 2 2 2 DG DG B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DG 4 4 4 DG DG B . n B 1 5 DC 5 5 5 DC DC B . n B 1 6 DG 6 6 6 DG DG B . 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 C 2 SPM 1 101 101 SPM SPM A . D 3 HOH 1 201 46 HOH HOH A . D 3 HOH 2 202 31 HOH HOH A . D 3 HOH 3 203 23 HOH HOH A . D 3 HOH 4 204 53 HOH HOH A . D 3 HOH 5 205 97 HOH HOH A . D 3 HOH 6 206 17 HOH HOH A . D 3 HOH 7 207 29 HOH HOH A . D 3 HOH 8 208 4 HOH HOH A . D 3 HOH 9 209 20 HOH HOH A . D 3 HOH 10 210 96 HOH HOH A . D 3 HOH 11 211 1 HOH HOH A . D 3 HOH 12 212 83 HOH HOH A . D 3 HOH 13 213 28 HOH HOH A . D 3 HOH 14 214 57 HOH HOH A . D 3 HOH 15 215 11 HOH HOH A . D 3 HOH 16 216 7 HOH HOH A . D 3 HOH 17 217 58 HOH HOH A . D 3 HOH 18 218 32 HOH HOH A . D 3 HOH 19 219 95 HOH HOH A . D 3 HOH 20 220 2 HOH HOH A . D 3 HOH 21 221 18 HOH HOH A . D 3 HOH 22 222 36 HOH HOH A . D 3 HOH 23 223 25 HOH HOH A . D 3 HOH 24 224 47 HOH HOH A . D 3 HOH 25 225 87 HOH HOH A . D 3 HOH 26 226 9 HOH HOH A . D 3 HOH 27 227 89 HOH HOH A . D 3 HOH 28 228 76 HOH HOH A . D 3 HOH 29 229 15 HOH HOH A . D 3 HOH 30 230 34 HOH HOH A . D 3 HOH 31 231 49 HOH HOH A . D 3 HOH 32 232 24 HOH HOH A . D 3 HOH 33 233 21 HOH HOH A . D 3 HOH 34 234 62 HOH HOH A . D 3 HOH 35 235 51 HOH HOH A . D 3 HOH 36 236 55 HOH HOH A . D 3 HOH 37 237 91 HOH HOH A . D 3 HOH 38 238 61 HOH HOH A . D 3 HOH 39 239 63 HOH HOH A . D 3 HOH 40 240 14 HOH HOH A . D 3 HOH 41 241 84 HOH HOH A . D 3 HOH 42 242 54 HOH HOH A . D 3 HOH 43 243 90 HOH HOH A . D 3 HOH 44 244 64 HOH HOH A . D 3 HOH 45 245 43 HOH HOH A . D 3 HOH 46 246 27 HOH HOH A . D 3 HOH 47 247 78 HOH HOH A . D 3 HOH 48 248 45 HOH HOH A . D 3 HOH 49 249 44 HOH HOH A . D 3 HOH 50 250 74 HOH HOH A . D 3 HOH 51 251 81 HOH HOH A . D 3 HOH 52 252 80 HOH HOH A . D 3 HOH 53 253 77 HOH HOH A . D 3 HOH 54 254 60 HOH HOH A . E 3 HOH 1 101 94 HOH HOH B . E 3 HOH 2 102 50 HOH HOH B . E 3 HOH 3 103 38 HOH HOH B . E 3 HOH 4 104 82 HOH HOH B . E 3 HOH 5 105 52 HOH HOH B . E 3 HOH 6 106 13 HOH HOH B . E 3 HOH 7 107 10 HOH HOH B . E 3 HOH 8 108 92 HOH HOH B . E 3 HOH 9 109 30 HOH HOH B . E 3 HOH 10 110 6 HOH HOH B . E 3 HOH 11 111 33 HOH HOH B . E 3 HOH 12 112 3 HOH HOH B . E 3 HOH 13 113 65 HOH HOH B . E 3 HOH 14 114 19 HOH HOH B . E 3 HOH 15 115 88 HOH HOH B . E 3 HOH 16 116 40 HOH HOH B . E 3 HOH 17 117 5 HOH HOH B . E 3 HOH 18 118 8 HOH HOH B . E 3 HOH 19 119 67 HOH HOH B . E 3 HOH 20 120 16 HOH HOH B . E 3 HOH 21 121 70 HOH HOH B . E 3 HOH 22 122 37 HOH HOH B . E 3 HOH 23 123 22 HOH HOH B . E 3 HOH 24 124 42 HOH HOH B . E 3 HOH 25 125 41 HOH HOH B . E 3 HOH 26 126 72 HOH HOH B . E 3 HOH 27 127 69 HOH HOH B . E 3 HOH 28 128 71 HOH HOH B . E 3 HOH 29 129 93 HOH HOH B . E 3 HOH 30 130 59 HOH HOH B . E 3 HOH 31 131 73 HOH HOH B . E 3 HOH 32 132 39 HOH HOH B . E 3 HOH 33 133 85 HOH HOH B . E 3 HOH 34 134 48 HOH HOH B . E 3 HOH 35 135 26 HOH HOH B . E 3 HOH 36 136 68 HOH HOH B . E 3 HOH 37 137 56 HOH HOH B . E 3 HOH 38 138 75 HOH HOH B . E 3 HOH 39 139 86 HOH HOH B . E 3 HOH 40 140 66 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? 'data collection' ? ? ? ? ? ? ? ? ? ? ? GDA ? ? ? . 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? xia2 ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? . 4 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.20.1_4487 5 ? 'model building' ? ? ? ? ? ? ? ? ? ? ? Coot ? ? ? . 6 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 8OE9 _cell.details ? _cell.formula_units_Z ? _cell.length_a 18.340 _cell.length_a_esd ? _cell.length_b 30.710 _cell.length_b_esd ? _cell.length_c 42.630 _cell.length_c_esd ? _cell.volume 24010.128 _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 8OE9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8OE9 _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.66 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 25.81 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.pdbx_mosaic_method ? _exptl_crystal.pdbx_mosaic_block_size ? _exptl_crystal.pdbx_mosaic_block_size_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'oligo, 2-methyl-2,4-pentanediol (MPD), sodium cacodylate, KCl, NaCl and spermine tetrachloride' _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.temp 291 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS EIGER2 XE 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2021-11-25 _diffrn_detector.pdbx_frequency ? _diffrn_detector.id ? _diffrn_detector.number_of_axes ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator ? _diffrn_radiation.polarisn_norm ? _diffrn_radiation.polarisn_ratio ? _diffrn_radiation.probe ? _diffrn_radiation.type ? _diffrn_radiation.xray_symbol ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_wavelength_list ? _diffrn_radiation.pdbx_wavelength ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_analyzer ? _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9763 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.current ? _diffrn_source.details ? _diffrn_source.diffrn_id 1 _diffrn_source.power ? _diffrn_source.size ? _diffrn_source.source SYNCHROTRON _diffrn_source.target ? _diffrn_source.type 'DIAMOND BEAMLINE I03' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9763 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline I03 _diffrn_source.pdbx_synchrotron_site Diamond # _reflns.B_iso_Wilson_estimate 9.12 _reflns.entry_id 8OE9 _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.04 _reflns.d_resolution_low 24.92 _reflns.details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.number_all ? _reflns.number_obs 11394 _reflns.observed_criterion ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.percent_possible_obs 94 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.6 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 6.7 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.996 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # _reflns_shell.d_res_high 1.04 _reflns_shell.d_res_low 1.06 _reflns_shell.meanI_over_sigI_all ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_possible ? _reflns_shell.number_unique_all ? _reflns_shell.number_unique_obs 327 _reflns_shell.percent_possible_obs ? _reflns_shell.Rmerge_F_all ? _reflns_shell.Rmerge_F_obs ? _reflns_shell.meanI_over_sigI_gt ? _reflns_shell.meanI_over_uI_all ? _reflns_shell.meanI_over_uI_gt ? _reflns_shell.number_measured_gt ? _reflns_shell.number_unique_gt ? _reflns_shell.percent_possible_gt ? _reflns_shell.Rmerge_F_gt ? _reflns_shell.Rmerge_I_gt ? _reflns_shell.pdbx_redundancy ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_netI_over_sigmaI_all ? _reflns_shell.pdbx_netI_over_sigmaI_obs ? _reflns_shell.pdbx_Rrim_I_all ? _reflns_shell.pdbx_Rpim_I_all ? _reflns_shell.pdbx_rejects ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_CC_half 0.357 _reflns_shell.pdbx_CC_star ? _reflns_shell.pdbx_R_split ? _reflns_shell.percent_possible_all ? _reflns_shell.Rmerge_I_all ? _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_percent_possible_ellipsoidal ? _reflns_shell.pdbx_percent_possible_spherical ? _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns_shell.pdbx_percent_possible_spherical_anomalous ? _reflns_shell.pdbx_redundancy_anomalous ? _reflns_shell.pdbx_CC_half_anomalous ? _reflns_shell.pdbx_absDiff_over_sigma_anomalous ? _reflns_shell.pdbx_percent_possible_anomalous ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean 16.47 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8OE9 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.04 _refine.ls_d_res_low 24.92 _refine.ls_extinction_coef ? _refine.ls_extinction_coef_esd ? _refine.ls_extinction_expression ? _refine.ls_extinction_method ? _refine.ls_goodness_of_fit_all ? _refine.ls_goodness_of_fit_all_esd ? _refine.ls_goodness_of_fit_obs ? _refine.ls_goodness_of_fit_obs_esd ? _refine.ls_hydrogen_treatment ? _refine.ls_matrix_type ? _refine.ls_number_constraints ? _refine.ls_number_parameters ? _refine.ls_number_reflns_all ? _refine.ls_number_reflns_obs 11327 _refine.ls_number_reflns_R_free 567 _refine.ls_number_reflns_R_work 10760 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 93.46 _refine.ls_percent_reflns_R_free 5.01 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1562 _refine.ls_R_factor_R_free 0.1779 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1551 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _refine.ls_R_factor_gt ? _refine.ls_goodness_of_fit_gt ? _refine.ls_goodness_of_fit_ref ? _refine.ls_shift_over_su_max ? _refine.ls_shift_over_su_max_lt ? _refine.ls_shift_over_su_mean ? _refine.ls_shift_over_su_mean_lt ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.34 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error 24.8342 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.1295 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.04 _refine_hist.d_res_low 24.92 _refine_hist.number_atoms_solvent 94 _refine_hist.number_atoms_total 348 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 240 _refine_hist.pdbx_number_atoms_ligand 14 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.0121 ? 321 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.3418 ? 486 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.0583 ? 53 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.0157 ? 14 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 29.6484 ? 145 ? f_dihedral_angle_d ? ? # _refine_ls_restr_ncs.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_restr_ncs.dom_id d_2 _refine_ls_restr_ncs.ncs_model_details ? _refine_ls_restr_ncs.rms_dev_B_iso ? _refine_ls_restr_ncs.rms_dev_position 0.67171057901 _refine_ls_restr_ncs.weight_B_iso ? _refine_ls_restr_ncs.weight_position ? _refine_ls_restr_ncs.pdbx_ordinal 1 _refine_ls_restr_ncs.pdbx_type 'Torsion NCS' _refine_ls_restr_ncs.pdbx_asym_id ? _refine_ls_restr_ncs.pdbx_auth_asym_id A _refine_ls_restr_ncs.pdbx_number ? _refine_ls_restr_ncs.pdbx_rms ? _refine_ls_restr_ncs.pdbx_weight ? _refine_ls_restr_ncs.pdbx_ens_id ens_1 # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.04 1.14 . . 109 2109 74.71 . . . . 0.3584 . . . . . . . . . . . 0.3512 'X-RAY DIFFRACTION' 1.14 1.31 . . 147 2813 99.30 . . . . 0.2486 . . . . . . . . . . . 0.2773 'X-RAY DIFFRACTION' 1.31 1.65 . . 152 2851 99.77 . . . . 0.1665 . . . . . . . . . . . 0.1523 'X-RAY DIFFRACTION' 1.65 24.92 . . 159 2987 99.59 . . . . 0.1080 . . . . . . . . . . . 0.1438 # _struct_ncs_oper.id 1 _struct_ncs_oper.code given _struct_ncs_oper.matrix[1][1] 0.189590196429 _struct_ncs_oper.matrix[1][2] 0.979478938684 _struct_ncs_oper.matrix[1][3] 0.0683854231027 _struct_ncs_oper.matrix[2][1] 0.980541769576 _struct_ncs_oper.matrix[2][2] -0.192487633862 _struct_ncs_oper.matrix[2][3] 0.0385531960576 _struct_ncs_oper.matrix[3][1] 0.0509253918411 _struct_ncs_oper.matrix[3][2] 0.0597454557689 _struct_ncs_oper.matrix[3][3] -0.996913780114 _struct_ncs_oper.vector[1] 3.43929096318 _struct_ncs_oper.vector[2] -3.91472723579 _struct_ncs_oper.vector[3] -5.84327745608 _struct_ncs_oper.details ? # loop_ _struct_ncs_dom.pdbx_ens_id _struct_ncs_dom.id _struct_ncs_dom.details ens_1 d_1 ;(chain "A" and (resid 2 or resid 4 through 6)) ; ens_1 d_2 ;(chain "B" and (resid 2 or resid 4 through 6)) ; # loop_ _struct_ncs_dom_lim.pdbx_ens_id _struct_ncs_dom_lim.dom_id _struct_ncs_dom_lim.pdbx_component_id _struct_ncs_dom_lim.beg_label_alt_id _struct_ncs_dom_lim.beg_label_asym_id _struct_ncs_dom_lim.beg_label_comp_id _struct_ncs_dom_lim.beg_label_seq_id _struct_ncs_dom_lim.end_label_alt_id _struct_ncs_dom_lim.end_label_asym_id _struct_ncs_dom_lim.end_label_comp_id _struct_ncs_dom_lim.end_label_seq_id _struct_ncs_dom_lim.beg_auth_asym_id _struct_ncs_dom_lim.beg_auth_seq_id _struct_ncs_dom_lim.end_auth_asym_id _struct_ncs_dom_lim.end_auth_seq_id _struct_ncs_dom_lim.pdbx_refine_code _struct_ncs_dom_lim.selection_details _struct_ncs_dom_lim.beg_auth_comp_id _struct_ncs_dom_lim.end_auth_comp_id ens_1 d_1 1 . A DG . . A DG . ? ? ? ? ? ? ? ? ens_1 d_2 1 . C DG . . C DG . ? ? ? ? ? ? ? ? # _struct_ncs_ens.id ens_1 _struct_ncs_ens.details ? # _struct_ncs_ens_gen.ens_id ens_1 _struct_ncs_ens_gen.dom_id_1 d_2 _struct_ncs_ens_gen.dom_id_2 d_1 _struct_ncs_ens_gen.oper_id 1 # _struct.entry_id 8OE9 _struct.title 'Crystal structure of the Z-DNA duplex d(CGCGCG) soaked in copper(II) chloride and hydrogen peroxide' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 8OE9 _struct_keywords.text DNA _struct_keywords.pdbx_keywords 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 8OE9 _struct_ref.pdbx_db_accession 8OE9 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 8OE9 A 1 ? 6 ? 8OE9 1 ? 6 ? 1 6 2 1 8OE9 B 1 ? 6 ? 8OE9 1 ? 6 ? 1 6 # _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 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 990 ? 1 MORE -1 ? 1 'SSA (A^2)' 2470 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 6 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 5 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 3 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 3 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 3 B DG 4 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 A ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 3 N3 B ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 A ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 3 O2 B ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 A ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 3 N4 B ? A DG 4 B DC 3 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 2 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 A ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 B ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 A ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 B ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 A ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 B ? A DG 6 B DC 1 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # _struct_conn_type.id hydrog _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 OP2 _pdbx_validate_symm_contact.auth_asym_id_1 B _pdbx_validate_symm_contact.auth_comp_id_1 DC _pdbx_validate_symm_contact.auth_seq_id_1 3 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 A _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 HN0 _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 SPM _pdbx_validate_symm_contact.auth_seq_id_2 101 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 4_545 _pdbx_validate_symm_contact.dist 1.53 # loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 x+1/2,-y+1/2,-z 3 -x,y+1/2,-z+1/2 4 -x+1/2,-y,z+1/2 # _pdbx_entry_details.entry_id 8OE9 _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_distant_solvent_atoms.id 1 _pdbx_distant_solvent_atoms.PDB_model_num 1 _pdbx_distant_solvent_atoms.auth_atom_id O _pdbx_distant_solvent_atoms.label_alt_id ? _pdbx_distant_solvent_atoms.auth_asym_id B _pdbx_distant_solvent_atoms.auth_comp_id HOH _pdbx_distant_solvent_atoms.auth_seq_id 140 _pdbx_distant_solvent_atoms.PDB_ins_code ? _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance 6.43 _pdbx_distant_solvent_atoms.neighbor_ligand_distance . # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 DG OP3 O N N 35 DG P P N N 36 DG OP1 O N N 37 DG OP2 O N N 38 DG "O5'" O N N 39 DG "C5'" C N N 40 DG "C4'" C N R 41 DG "O4'" O N N 42 DG "C3'" C N S 43 DG "O3'" O N N 44 DG "C2'" C N N 45 DG "C1'" C N R 46 DG N9 N Y N 47 DG C8 C Y N 48 DG N7 N Y N 49 DG C5 C Y N 50 DG C6 C N N 51 DG O6 O N N 52 DG N1 N N N 53 DG C2 C N N 54 DG N2 N N N 55 DG N3 N N N 56 DG C4 C Y N 57 DG HOP3 H N N 58 DG HOP2 H N N 59 DG "H5'" H N N 60 DG "H5''" H N N 61 DG "H4'" H N N 62 DG "H3'" H N N 63 DG "HO3'" H N N 64 DG "H2'" H N N 65 DG "H2''" H N N 66 DG "H1'" H N N 67 DG H8 H N N 68 DG H1 H N N 69 DG H21 H N N 70 DG H22 H N N 71 HOH O O N N 72 HOH H1 H N N 73 HOH H2 H N N 74 SPM N1 N N N 75 SPM C2 C N N 76 SPM C3 C N N 77 SPM C4 C N N 78 SPM N5 N N N 79 SPM C6 C N N 80 SPM C7 C N N 81 SPM C8 C N N 82 SPM C9 C N N 83 SPM N10 N N N 84 SPM C11 C N N 85 SPM C12 C N N 86 SPM C13 C N N 87 SPM N14 N N N 88 SPM HN11 H N N 89 SPM HN12 H N N 90 SPM H21 H N N 91 SPM H22 H N N 92 SPM H31 H N N 93 SPM H32 H N N 94 SPM H41 H N N 95 SPM H42 H N N 96 SPM HN5 H N N 97 SPM H61 H N N 98 SPM H62 H N N 99 SPM H71 H N N 100 SPM H72 H N N 101 SPM H81 H N N 102 SPM H82 H N N 103 SPM H91 H N N 104 SPM H92 H N N 105 SPM HN0 H N N 106 SPM H111 H N N 107 SPM H112 H N N 108 SPM H121 H N N 109 SPM H122 H N N 110 SPM H131 H N N 111 SPM H132 H N N 112 SPM HN41 H N N 113 SPM HN42 H N N 114 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 DG OP3 P sing N N 36 DG OP3 HOP3 sing N N 37 DG P OP1 doub N N 38 DG P OP2 sing N N 39 DG P "O5'" sing N N 40 DG OP2 HOP2 sing N N 41 DG "O5'" "C5'" sing N N 42 DG "C5'" "C4'" sing N N 43 DG "C5'" "H5'" sing N N 44 DG "C5'" "H5''" sing N N 45 DG "C4'" "O4'" sing N N 46 DG "C4'" "C3'" sing N N 47 DG "C4'" "H4'" sing N N 48 DG "O4'" "C1'" sing N N 49 DG "C3'" "O3'" sing N N 50 DG "C3'" "C2'" sing N N 51 DG "C3'" "H3'" sing N N 52 DG "O3'" "HO3'" sing N N 53 DG "C2'" "C1'" sing N N 54 DG "C2'" "H2'" sing N N 55 DG "C2'" "H2''" sing N N 56 DG "C1'" N9 sing N N 57 DG "C1'" "H1'" sing N N 58 DG N9 C8 sing Y N 59 DG N9 C4 sing Y N 60 DG C8 N7 doub Y N 61 DG C8 H8 sing N N 62 DG N7 C5 sing Y N 63 DG C5 C6 sing N N 64 DG C5 C4 doub Y N 65 DG C6 O6 doub N N 66 DG C6 N1 sing N N 67 DG N1 C2 sing N N 68 DG N1 H1 sing N N 69 DG C2 N2 sing N N 70 DG C2 N3 doub N N 71 DG N2 H21 sing N N 72 DG N2 H22 sing N N 73 DG N3 C4 sing N N 74 HOH O H1 sing N N 75 HOH O H2 sing N N 76 SPM N1 C2 sing N N 77 SPM N1 HN11 sing N N 78 SPM N1 HN12 sing N N 79 SPM C2 C3 sing N N 80 SPM C2 H21 sing N N 81 SPM C2 H22 sing N N 82 SPM C3 C4 sing N N 83 SPM C3 H31 sing N N 84 SPM C3 H32 sing N N 85 SPM C4 N5 sing N N 86 SPM C4 H41 sing N N 87 SPM C4 H42 sing N N 88 SPM N5 C6 sing N N 89 SPM N5 HN5 sing N N 90 SPM C6 C7 sing N N 91 SPM C6 H61 sing N N 92 SPM C6 H62 sing N N 93 SPM C7 C8 sing N N 94 SPM C7 H71 sing N N 95 SPM C7 H72 sing N N 96 SPM C8 C9 sing N N 97 SPM C8 H81 sing N N 98 SPM C8 H82 sing N N 99 SPM C9 N10 sing N N 100 SPM C9 H91 sing N N 101 SPM C9 H92 sing N N 102 SPM N10 C11 sing N N 103 SPM N10 HN0 sing N N 104 SPM C11 C12 sing N N 105 SPM C11 H111 sing N N 106 SPM C11 H112 sing N N 107 SPM C12 C13 sing N N 108 SPM C12 H121 sing N N 109 SPM C12 H122 sing N N 110 SPM C13 N14 sing N N 111 SPM C13 H131 sing N N 112 SPM C13 H132 sing N N 113 SPM N14 HN41 sing N N 114 SPM N14 HN42 sing N N 115 # _ndb_struct_conf_na.entry_id 8OE9 _ndb_struct_conf_na.feature 'z-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 DC 1 1_555 B DG 6 1_555 -0.201 -0.133 0.118 1.951 -1.340 3.166 1 A_DC1:DG6_B A 1 ? B 6 ? 19 1 1 A DG 2 1_555 B DC 5 1_555 0.264 -0.184 0.106 -3.577 2.703 2.198 2 A_DG2:DC5_B A 2 ? B 5 ? 19 1 1 A DC 3 1_555 B DG 4 1_555 -0.345 -0.133 0.053 3.700 6.305 3.086 3 A_DC3:DG4_B A 3 ? B 4 ? 19 1 1 A DG 4 1_555 B DC 3 1_555 0.249 -0.156 0.571 2.745 1.449 2.933 4 A_DG4:DC3_B A 4 ? B 3 ? 19 1 1 A DC 5 1_555 B DG 2 1_555 -0.225 -0.215 0.005 5.868 -5.471 2.006 5 A_DC5:DG2_B A 5 ? B 2 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 0.171 -0.248 -0.058 -5.783 3.755 3.250 6 A_DG6:DC1_B A 6 ? B 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 B DG 6 1_555 A DG 2 1_555 B DC 5 1_555 0.266 5.460 3.582 2.108 -1.701 -9.098 -28.616 7.032 4.351 10.425 12.917 -9.492 1 AA_DC1DG2:DC5DG6_BB A 1 ? B 6 ? A 2 ? B 5 ? 1 A DG 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 0.600 -0.400 3.192 0.913 -6.320 -54.652 0.796 0.703 3.122 6.857 0.990 -54.996 2 AA_DG2DC3:DG4DC5_BB A 2 ? B 5 ? A 3 ? B 4 ? 1 A DC 3 1_555 B DG 4 1_555 A DG 4 1_555 B DC 3 1_555 -0.431 5.383 3.586 -5.141 2.331 -7.234 -37.922 -12.097 1.222 -15.696 -34.615 -9.173 3 AA_DC3DG4:DC3DG4_BB A 3 ? B 4 ? A 4 ? B 3 ? 1 A DG 4 1_555 B DC 3 1_555 A DC 5 1_555 B DG 2 1_555 -0.576 -1.160 3.477 4.527 -0.736 -51.470 1.385 -0.333 3.497 0.846 5.201 -51.660 4 AA_DG4DC5:DG2DC3_BB A 4 ? B 3 ? A 5 ? B 2 ? 1 A DC 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 0.097 5.625 3.791 2.543 1.035 -7.641 -42.793 8.211 2.822 -7.455 18.319 -8.118 5 AA_DC5DG6:DC1DG2_BB A 5 ? B 2 ? A 6 ? B 1 ? # _pdbx_audit_support.funding_organization 'Engineering and Physical Sciences Research Council' _pdbx_audit_support.country 'United Kingdom' _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 1I0T _pdbx_initial_refinement_model.details ? # _space_group.name_H-M_alt 'P 21 21 21' _space_group.name_Hall 'P 2ac 2ab' _space_group.IT_number 19 _space_group.crystal_system orthorhombic _space_group.id 1 # _atom_sites.entry_id 8OE9 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.054526 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032563 _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] 0.023458 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol _atom_type.scat_dispersion_real _atom_type.scat_dispersion_imag _atom_type.scat_Cromer_Mann_a1 _atom_type.scat_Cromer_Mann_a2 _atom_type.scat_Cromer_Mann_a3 _atom_type.scat_Cromer_Mann_a4 _atom_type.scat_Cromer_Mann_b1 _atom_type.scat_Cromer_Mann_b2 _atom_type.scat_Cromer_Mann_b3 _atom_type.scat_Cromer_Mann_b4 _atom_type.scat_Cromer_Mann_c _atom_type.scat_source _atom_type.scat_dispersion_source C ? ? 3.54356 2.42580 ? ? 25.62398 1.50364 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? H ? ? 0.53795 0.34799 0.11320 ? 10.08003 29.74760 2.57510 ? 0.0 ;3-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? N ? ? 4.01032 2.96436 ? ? 19.97189 1.75589 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? O ? ? 4.49882 3.47563 ? ? 15.80542 1.70748 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? P ? ? 9.51135 5.44231 ? ? 1.42069 35.72801 ? ? 0.0 ;2-Gaussian fit: Grosse-Kunstleve RW, Sauter NK, Adams PD: Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3, 22-31. ; ? # loop_