data_7YGO # _entry.id 7YGO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.368 _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 7YGO pdb_00007ygo 10.2210/pdb7ygo/pdb WWPDB D_1300030885 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7YGO _pdbx_database_status.recvd_initial_deposition_date 2022-07-12 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kondo, J.' 1 0000-0002-5682-3685 'Torigoe, H.' 2 ? 'Arakawa, F.' 3 ? # _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 US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev J.Inorg.Biochem. _citation.journal_id_ASTM JIBIDJ _citation.journal_id_CSD 0525 _citation.journal_id_ISSN 0162-0134 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 241 _citation.language ? _citation.page_first 112125 _citation.page_last 112125 _citation.title 'Specific binding of Hg 2+ to mismatched base pairs involving 5-hydroxyuracil in duplex DNA.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1016/j.jinorgbio.2023.112125 _citation.pdbx_database_id_PubMed 36716510 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Torigoe, H.' 1 ? primary 'Kondo, J.' 2 ? primary 'Arakawa, F.' 3 ? # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 120.000 _cell.angle_gamma_esd ? _cell.entry_id 7YGO _cell.details ? _cell.formula_units_Z ? _cell.length_a 37.336 _cell.length_a_esd ? _cell.length_b 37.336 _cell.length_b_esd ? _cell.length_c 54.938 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 6 _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 7YGO _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' _symmetry.pdbx_full_space_group_name_H-M ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*GP*GP*AP*CP*CP*TP*(6HU)P*GP*GP*TP*CP*C)-3') ; 3656.351 1 ? ? ? ? 2 non-polymer syn 'MERCURY (II) ION' 200.590 1 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DG)(DG)(DA)(DC)(DC)(DT)(OHU)(DG)(DG)(DT)(DC)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GGACCTXGGTCC _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DG n 1 2 DG n 1 3 DA n 1 4 DC n 1 5 DC n 1 6 DT n 1 7 OHU n 1 8 DG n 1 9 DG n 1 10 DT n 1 11 DC n 1 12 DC 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 12 _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 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7YGO _struct_ref.pdbx_db_accession 7YGO _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7YGO _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 12 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7YGO _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 12 _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 12 # 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 HG non-polymer . 'MERCURY (II) ION' ? 'Hg 2' 200.590 OHU 'DNA linking' n ;2'-deoxy-5-hydroxyuridine 5'-(dihydrogen phosphate) ; ? 'C9 H13 N2 O9 P' 324.181 # _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 7YGO _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 3.02 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 59.31 _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, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'MPD, spermine, potassium nitrate, MOPS' _exptl_crystal_grow.pdbx_pH_range ? # _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 PILATUS3 S 6M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2018-11-21 _diffrn_detector.pdbx_frequency ? # _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 1.00910 _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 'PHOTON FACTORY BEAMLINE BL-5A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 1.00910 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-5A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 71.070 _reflns.entry_id 7YGO _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.400 _reflns.d_resolution_low 27.866 _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 3345 _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 99.800 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 10.032 _reflns.pdbx_Rmerge_I_obs 0.036 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 30.950 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.568 _reflns.pdbx_scaling_rejects 11 _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 0.038 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 33557 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.999 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _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.pdbx_CC_split_method ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _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 _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_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_Rsym_value _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 _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _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 2.400 2.470 ? 4.700 ? 2426 276 ? 273 98.900 ? ? ? ? 0.304 ? ? ? ? ? ? ? ? 8.886 ? ? ? ? 0.323 ? ? 1 1 0.992 ? ? ? ? ? ? ? ? ? ? 2.470 2.540 ? 6.600 ? 2309 227 ? 227 100.000 ? ? ? ? 0.271 ? ? ? ? ? ? ? ? 10.172 ? ? ? ? 0.285 ? ? 2 1 0.988 ? ? ? ? ? ? ? ? ? ? 2.540 2.620 ? 8.970 ? 2548 253 ? 253 100.000 ? ? ? ? 0.185 ? ? ? ? ? ? ? ? 10.071 ? ? ? ? 0.195 ? ? 3 1 0.996 ? ? ? ? ? ? ? ? ? ? 2.620 2.700 ? 12.030 ? 2587 247 ? 247 100.000 ? ? ? ? 0.142 ? ? ? ? ? ? ? ? 10.474 ? ? ? ? 0.150 ? ? 4 1 0.997 ? ? ? ? ? ? ? ? ? ? 2.700 2.800 ? 14.190 ? 2448 224 ? 223 99.600 ? ? ? ? 0.121 ? ? ? ? ? ? ? ? 10.978 ? ? ? ? 0.127 ? ? 5 1 0.998 ? ? ? ? ? ? ? ? ? ? 2.800 2.910 ? 18.600 ? 2705 248 ? 248 100.000 ? ? ? ? 0.093 ? ? ? ? ? ? ? ? 10.907 ? ? ? ? 0.098 ? ? 6 1 0.999 ? ? ? ? ? ? ? ? ? ? 2.910 3.020 ? 30.000 ? 2085 193 ? 193 100.000 ? ? ? ? 0.049 ? ? ? ? ? ? ? ? 10.803 ? ? ? ? 0.051 ? ? 7 1 1.000 ? ? ? ? ? ? ? ? ? ? 3.020 3.160 ? 35.080 ? 2265 215 ? 215 100.000 ? ? ? ? 0.044 ? ? ? ? ? ? ? ? 10.535 ? ? ? ? 0.047 ? ? 8 1 0.999 ? ? ? ? ? ? ? ? ? ? 3.160 3.310 ? 40.240 ? 1969 193 ? 193 100.000 ? ? ? ? 0.034 ? ? ? ? ? ? ? ? 10.202 ? ? ? ? 0.035 ? ? 9 1 1.000 ? ? ? ? ? ? ? ? ? ? 3.310 3.490 ? 42.570 ? 1651 176 ? 176 100.000 ? ? ? ? 0.035 ? ? ? ? ? ? ? ? 9.381 ? ? ? ? 0.038 ? ? 10 1 1.000 ? ? ? ? ? ? ? ? ? ? 3.490 3.700 ? 50.090 ? 1764 190 ? 190 100.000 ? ? ? ? 0.035 ? ? ? ? ? ? ? ? 9.284 ? ? ? ? 0.037 ? ? 11 1 1.000 ? ? ? ? ? ? ? ? ? ? 3.700 3.960 ? 46.970 ? 1447 154 ? 154 100.000 ? ? ? ? 0.033 ? ? ? ? ? ? ? ? 9.396 ? ? ? ? 0.034 ? ? 12 1 1.000 ? ? ? ? ? ? ? ? ? ? 3.960 4.280 ? 54.350 ? 1635 161 ? 161 100.000 ? ? ? ? 0.037 ? ? ? ? ? ? ? ? 10.155 ? ? ? ? 0.039 ? ? 13 1 1.000 ? ? ? ? ? ? ? ? ? ? 4.280 4.690 ? 55.720 ? 1528 154 ? 154 100.000 ? ? ? ? 0.033 ? ? ? ? ? ? ? ? 9.922 ? ? ? ? 0.034 ? ? 14 1 0.999 ? ? ? ? ? ? ? ? ? ? 4.690 5.240 ? 58.570 ? 1162 116 ? 116 100.000 ? ? ? ? 0.035 ? ? ? ? ? ? ? ? 10.017 ? ? ? ? 0.036 ? ? 15 1 0.999 ? ? ? ? ? ? ? ? ? ? 5.240 6.050 ? 56.940 ? 1087 113 ? 113 100.000 ? ? ? ? 0.031 ? ? ? ? ? ? ? ? 9.619 ? ? ? ? 0.032 ? ? 16 1 0.999 ? ? ? ? ? ? ? ? ? ? 6.050 7.410 ? 55.080 ? 880 100 ? 100 100.000 ? ? ? ? 0.030 ? ? ? ? ? ? ? ? 8.800 ? ? ? ? 0.032 ? ? 17 1 1.000 ? ? ? ? ? ? ? ? ? ? 7.410 10.480 ? 55.820 ? 677 72 ? 72 100.000 ? ? ? ? 0.029 ? ? ? ? ? ? ? ? 9.403 ? ? ? ? 0.031 ? ? 18 1 1.000 ? ? ? ? ? ? ? ? ? ? 10.480 27.866 ? 62.140 ? 384 40 ? 37 92.500 ? ? ? ? 0.031 ? ? ? ? ? ? ? ? 10.378 ? ? ? ? 0.033 ? ? 19 1 0.999 ? ? ? ? ? ? ? ? ? ? # _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 92.160 _refine.B_iso_mean 72.6245 _refine.B_iso_min 60.810 _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 7YGO _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 2.4030 _refine.ls_d_res_low 27.8660 _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 3336 _refine.ls_number_reflns_R_free 337 _refine.ls_number_reflns_R_work 2999 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.5200 _refine.ls_percent_reflns_R_free 10.1000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2078 _refine.ls_R_factor_R_free 0.2370 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.2045 _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 1.430 _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 THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _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 31.8100 _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 0.1500 _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 final _refine_hist.details ? _refine_hist.d_res_high 2.4030 _refine_hist.d_res_low 27.8660 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 243 _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 12 _refine_hist.pdbx_B_iso_mean_ligand 81.86 _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 242 _refine_hist.pdbx_number_atoms_ligand 1 _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' ? 0.008 ? 270 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 0.939 ? 415 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.041 ? 46 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.005 ? 12 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 17.020 ? 110 ? f_dihedral_angle_d ? ? # 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 _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 'X-RAY DIFFRACTION' 2.4030 3.0265 . . 165 1492 99.0000 . . . 0.3040 0.0000 0.2808 . . . . . . . . . . . 'X-RAY DIFFRACTION' 3.0265 27.8660 . . 172 1507 100.0000 . . . 0.2241 0.0000 0.1908 . . . . . . . . . . . # _struct.entry_id 7YGO _struct.title 'DNA duplex containing 5OHU-Hg(II)-T base pairs' _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 7YGO _struct_keywords.text 'DNA, metal-mediated base pair, metallo-DNA, mercury' _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 2 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DT 6 "O3'" ? ? ? 1_555 A OHU 7 P ? ? A DT 6 A OHU 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale one ? A OHU 7 "O3'" ? ? ? 1_555 A DG 8 P ? ? A OHU 7 A DG 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? metalc1 metalc ? ? A DT 6 N3 ? ? ? 1_555 B HG . HG ? ? A DT 6 A HG 101 1_555 ? ? ? ? ? ? ? 2.032 ? ? metalc2 metalc ? ? A DT 6 O4 ? ? ? 1_555 B HG . HG ? ? A DT 6 A HG 101 1_555 ? ? ? ? ? ? ? 2.576 ? ? metalc3 metalc ? ? A OHU 7 N3 ? ? ? 1_555 B HG . HG ? ? A OHU 7 A HG 101 6_557 ? ? ? ? ? ? ? 2.133 ? ? metalc4 metalc ? ? A OHU 7 O4 ? ? ? 1_555 B HG . HG ? ? A OHU 7 A HG 101 6_557 ? ? ? ? ? ? ? 2.825 ? ? metalc5 metalc ? ? A DG 8 O6 ? ? ? 1_555 B HG . HG ? ? A DG 8 A HG 101 6_557 ? ? ? ? ? ? ? 3.047 ? ? hydrog1 hydrog ? ? A DG 1 N1 ? ? ? 1_555 A DC 12 N3 ? ? A DG 1 A DC 12 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 1 N2 ? ? ? 1_555 A DC 12 O2 ? ? A DG 1 A DC 12 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 1 O6 ? ? ? 1_555 A DC 12 N4 ? ? A DG 1 A DC 12 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 A DC 11 N3 ? ? A DG 2 A DC 11 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 A DC 11 O2 ? ? A DG 2 A DC 11 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 A DC 11 N4 ? ? A DG 2 A DC 11 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 3 N1 ? ? ? 1_555 A DT 10 N3 ? ? A DA 3 A DT 10 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DA 3 N6 ? ? ? 1_555 A DT 10 O4 ? ? A DA 3 A DT 10 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 4 N3 ? ? ? 1_555 A DG 9 N1 ? ? A DC 4 A DG 9 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 4 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 4 A DG 9 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DC 4 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 4 A DG 9 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 8 N1 ? ? A DC 5 A DG 8 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 8 O6 ? ? A DC 5 A DG 8 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 8 N2 ? ? A DC 5 A DG 8 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 8 N1 ? ? ? 1_555 A DC 5 N3 ? ? A DG 8 A DC 5 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 8 N2 ? ? ? 1_555 A DC 5 O2 ? ? A DG 8 A DC 5 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DG 8 O6 ? ? ? 1_555 A DC 5 N4 ? ? A DG 8 A DC 5 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DG 9 N1 ? ? ? 1_555 A DC 4 N3 ? ? A DG 9 A DC 4 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DG 9 N2 ? ? ? 1_555 A DC 4 O2 ? ? A DG 9 A DC 4 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DC 4 N4 ? ? A DG 9 A DC 4 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DT 10 N3 ? ? ? 1_555 A DA 3 N1 ? ? A DT 10 A DA 3 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DT 10 O4 ? ? ? 1_555 A DA 3 N6 ? ? A DT 10 A DA 3 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 11 N3 ? ? ? 1_555 A DG 2 N1 ? ? A DC 11 A DG 2 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 11 N4 ? ? ? 1_555 A DG 2 O6 ? ? A DC 11 A DG 2 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 11 O2 ? ? ? 1_555 A DG 2 N2 ? ? A DC 11 A DG 2 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 12 N3 ? ? ? 1_555 A DG 1 N1 ? ? A DC 12 A DG 1 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 12 N4 ? ? ? 1_555 A DG 1 O6 ? ? A DC 12 A DG 1 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 12 O2 ? ? ? 1_555 A DG 1 N2 ? ? A DC 12 A DG 1 6_557 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _atom_sites.entry_id 7YGO _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] 0.026784 _atom_sites.fract_transf_matrix[1][2] 0.015464 _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] 0.030927 _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] 0.018202 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C HG N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DG 1 1 1 DG DG A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DA 3 3 3 DA DA A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 DT 6 6 6 DT DT A . n A 1 7 OHU 7 7 7 OHU 6HU A . n A 1 8 DG 8 8 8 DG DG A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DT 10 10 10 DT DT A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DC 12 12 12 DC DC A . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email j.kondo@sophia.ac.jp _pdbx_contact_author.name_first Jiro _pdbx_contact_author.name_last Kondo _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0002-5682-3685 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id HG _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 101 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id HG _pdbx_nonpoly_scheme.auth_mon_id HG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 1510 ? 1 MORE -68 ? 1 'SSA (A^2)' 4270 ? # 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' 6_557 -x,-x+y,-z+7/3 -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 128.1886666667 # 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 N3 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O4 ? A DT 6 ? A DT 6 ? 1_555 57.6 ? 2 N3 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 N3 ? A OHU 7 ? A OHU 7 ? 1_555 81.4 ? 3 O4 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 N3 ? A OHU 7 ? A OHU 7 ? 1_555 86.8 ? 4 N3 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O4 ? A OHU 7 ? A OHU 7 ? 1_555 69.6 ? 5 O4 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O4 ? A OHU 7 ? A OHU 7 ? 1_555 52.7 ? 6 N3 ? A OHU 7 ? A OHU 7 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O4 ? A OHU 7 ? A OHU 7 ? 1_555 34.6 ? 7 N3 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O6 ? A DG 8 ? A DG 8 ? 1_555 99.9 ? 8 O4 ? A DT 6 ? A DT 6 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O6 ? A DG 8 ? A DG 8 ? 1_555 71.9 ? 9 N3 ? A OHU 7 ? A OHU 7 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O6 ? A DG 8 ? A DG 8 ? 1_555 35.6 ? 10 O4 ? A OHU 7 ? A OHU 7 ? 1_555 HG ? B HG . ? A HG 101 ? 1_555 O6 ? A DG 8 ? A DG 8 ? 1_555 30.5 ? # _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 2023-05-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _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 scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 1 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? 1.17.1 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _pdbx_entry_details.entry_id 7YGO _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 7YGO 'double helix' 7YGO 'a-form double helix' 7YGO 'internal loop' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DG 1 1_555 A DC 12 6_557 -0.683 0.022 0.182 -5.494 -8.728 6.884 1 A_DG1:DC12_A A 1 ? A 12 ? 19 1 1 A DG 2 1_555 A DC 11 6_557 -0.613 -0.307 -0.474 -14.557 -17.232 2.402 2 A_DG2:DC11_A A 2 ? A 11 ? 19 1 1 A DA 3 1_555 A DT 10 6_557 0.367 -0.265 -0.352 -8.987 -7.724 -4.169 3 A_DA3:DT10_A A 3 ? A 10 ? 20 1 1 A DC 4 1_555 A DG 9 6_557 0.004 0.027 -0.048 8.695 -6.998 1.888 4 A_DC4:DG9_A A 4 ? A 9 ? 19 1 1 A DC 5 1_555 A DG 8 6_557 0.373 -0.429 -0.138 13.022 -5.355 1.361 5 A_DC5:DG8_A A 5 ? A 8 ? 19 1 1 A DG 1 6_557 A DC 12 1_555 -0.683 0.022 0.182 -5.494 -8.728 6.884 6 A_DG1:DC12_A A 1 ? A 12 ? 19 1 1 A DG 2 6_557 A DC 11 1_555 -0.613 -0.307 -0.474 -14.557 -17.232 2.402 7 A_DG2:DC11_A A 2 ? A 11 ? 19 1 1 A DA 3 6_557 A DT 10 1_555 0.367 -0.265 -0.352 -8.987 -7.724 -4.169 8 A_DA3:DT10_A A 3 ? A 10 ? 20 1 1 A DC 4 6_557 A DG 9 1_555 0.004 0.027 -0.048 8.695 -6.998 1.888 9 A_DC4:DG9_A A 4 ? A 9 ? 19 1 1 A DC 5 6_557 A DG 8 1_555 0.373 -0.429 -0.138 13.022 -5.355 1.361 10 A_DC5:DG8_A A 5 ? A 8 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DG 1 1_555 A DC 12 6_557 A DG 2 1_555 A DC 11 6_557 0.079 -1.144 3.546 7.489 5.956 38.586 -2.421 0.810 3.299 8.848 -11.126 39.711 1 AA_DG1DG2:DC11DC12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A DG 2 1_555 A DC 11 6_557 A DA 3 1_555 A DT 10 6_557 -0.496 -0.562 3.135 -0.169 3.671 37.572 -1.319 0.746 3.071 5.683 0.262 37.745 2 AA_DG2DA3:DT10DC11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A DA 3 1_555 A DT 10 6_557 A DC 4 1_555 A DG 9 6_557 1.080 -1.320 2.886 -2.578 11.661 28.365 -4.304 -2.439 2.089 22.574 4.989 30.729 3 AA_DA3DC4:DG9DT10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A DC 4 1_555 A DG 9 6_557 A DC 5 1_555 A DG 8 6_557 -0.514 -1.735 3.193 -1.166 6.864 28.129 -4.861 0.791 2.720 13.856 2.353 28.961 4 AA_DC4DC5:DG8DG9_AA A 4 ? A 9 ? A 5 ? A 8 ? 1 A DG 1 6_557 A DC 12 1_555 A DG 2 6_557 A DC 11 1_555 0.079 -1.144 3.546 7.489 5.956 38.586 -2.421 0.810 3.299 8.848 -11.126 39.711 5 AA_DG1DG2:DC11DC12_AA A 1 ? A 12 ? A 2 ? A 11 ? 1 A DG 2 6_557 A DC 11 1_555 A DA 3 6_557 A DT 10 1_555 -0.496 -0.562 3.135 -0.169 3.671 37.572 -1.319 0.746 3.071 5.683 0.262 37.745 6 AA_DG2DA3:DT10DC11_AA A 2 ? A 11 ? A 3 ? A 10 ? 1 A DA 3 6_557 A DT 10 1_555 A DC 4 6_557 A DG 9 1_555 1.080 -1.320 2.886 -2.578 11.661 28.365 -4.304 -2.439 2.089 22.574 4.989 30.729 7 AA_DA3DC4:DG9DT10_AA A 3 ? A 10 ? A 4 ? A 9 ? 1 A DC 4 6_557 A DG 9 1_555 A DC 5 6_557 A DG 8 1_555 -0.514 -1.735 3.193 -1.166 6.864 28.129 -4.861 0.791 2.720 13.856 2.353 28.961 8 AA_DC4DC5:DG8DG9_AA A 4 ? A 9 ? A 5 ? A 8 ? # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 18K19308 _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id OHU _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id OHU _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'MERCURY (II) ION' _pdbx_entity_nonpoly.comp_id HG # _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 ? #