data_7XKM # _entry.id 7XKM # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.361 _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 7XKM pdb_00007xkm 10.2210/pdb7xkm/pdb WWPDB D_1300029056 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7XKM _pdbx_database_status.recvd_initial_deposition_date 2022-04-20 _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 'Ono, A.' 2 ? 'Atsugi, T.' 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 GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Angew.Chem.Int.Ed.Engl. _citation.journal_id_ASTM ACIEAY _citation.journal_id_CSD 0179 _citation.journal_id_ISSN 1521-3773 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 61 _citation.language ? _citation.page_first e202204798 _citation.page_last e202204798 _citation.title 'A Novel Ag I -DNA Rod Comprising a One-Dimensional Array of 11 Silver Ions within a Double Helical Structure.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/anie.202204798 _citation.pdbx_database_id_PubMed 35641885 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Atsugi, T.' 1 ? primary 'Ono, A.' 2 0000-0002-2150-7084 primary 'Tasaka, M.' 3 ? primary 'Eguchi, N.' 4 ? primary 'Fujiwara, S.' 5 0000-0002-4633-5872 primary 'Kondo, J.' 6 0000-0002-5682-3685 # _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 7XKM _cell.details ? _cell.formula_units_Z ? _cell.length_a 77.461 _cell.length_a_esd ? _cell.length_b 77.461 _cell.length_b_esd ? _cell.length_c 123.722 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 48 _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 7XKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' _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(*CP*GP*CP*GP*CP*(BRU)P*CP*(BRU)P*CP*GP*CP*G)-3') ; 3745.082 4 ? ? ? ? 2 non-polymer syn 'SILVER ION' 107.868 23 ? ? ? ? 3 water nat water 18.015 6 ? ? ? ? # _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 '(DC)(DG)(DC)(DG)(DC)(BRU)(DC)(BRU)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGCUCUCGCG _entity_poly.pdbx_strand_id A,B,C,D _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DC n 1 4 DG n 1 5 DC n 1 6 BRU n 1 7 DC n 1 8 BRU n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 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 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 7XKM _struct_ref.pdbx_db_accession 7XKM _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 7XKM A 1 ? 12 ? 7XKM 1 ? 12 ? 1 12 2 1 7XKM B 1 ? 12 ? 7XKM 1 ? 12 ? 1 12 3 1 7XKM C 1 ? 12 ? 7XKM 1 ? 12 ? 1 12 4 1 7XKM D 1 ? 12 ? 7XKM 1 ? 12 ? 1 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 AG non-polymer . 'SILVER ION' ? 'Ag 1' 107.868 BRU 'DNA linking' n "5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" ? 'C9 H12 Br N2 O8 P' 387.078 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 # _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 7XKM _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 3.58 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 65.61 _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, MOPS, lithium nitrate' _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 2018-05-18 _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 0.91973 _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 0.91973 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-5A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 41.924 _reflns.entry_id 7XKM _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 2.790 _reflns.d_resolution_low 36.960 _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 10286 _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 99.900 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 21.109 _reflns.pdbx_Rmerge_I_obs 0.115 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 22.550 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.275 _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 0.117 _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 1.000 _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 2.800 2.870 ? 10.430 ? 15001 767 ? 764 99.600 ? ? ? ? 0.257 ? ? ? ? ? ? ? ? 19.635 ? ? ? ? 0.264 ? ? 1 1 0.997 ? ? ? ? ? ? ? ? ? ? 2.870 2.950 ? 9.070 ? 15715 723 ? 723 100.000 ? ? ? ? 0.344 ? ? ? ? ? ? ? ? 21.736 ? ? ? ? 0.352 ? ? 2 1 0.994 ? ? ? ? ? ? ? ? ? ? 2.950 3.030 ? 10.920 ? 15900 731 ? 731 100.000 ? ? ? ? 0.291 ? ? ? ? ? ? ? ? 21.751 ? ? ? ? 0.298 ? ? 3 1 0.995 ? ? ? ? ? ? ? ? ? ? 3.030 3.130 ? 12.780 ? 14879 691 ? 691 100.000 ? ? ? ? 0.239 ? ? ? ? ? ? ? ? 21.533 ? ? ? ? 0.244 ? ? 4 1 0.996 ? ? ? ? ? ? ? ? ? ? 3.130 3.230 ? 14.010 ? 14768 687 ? 687 100.000 ? ? ? ? 0.208 ? ? ? ? ? ? ? ? 21.496 ? ? ? ? 0.213 ? ? 5 1 0.998 ? ? ? ? ? ? ? ? ? ? 3.230 3.340 ? 13.600 ? 14000 652 ? 652 100.000 ? ? ? ? 0.222 ? ? ? ? ? ? ? ? 21.472 ? ? ? ? 0.227 ? ? 6 1 0.997 ? ? ? ? ? ? ? ? ? ? 3.340 3.470 ? 13.530 ? 13197 638 ? 638 100.000 ? ? ? ? 0.239 ? ? ? ? ? ? ? ? 20.685 ? ? ? ? 0.245 ? ? 7 1 0.996 ? ? ? ? ? ? ? ? ? ? 3.470 3.610 ? 17.750 ? 12222 609 ? 609 100.000 ? ? ? ? 0.166 ? ? ? ? ? ? ? ? 20.069 ? ? ? ? 0.170 ? ? 8 1 0.998 ? ? ? ? ? ? ? ? ? ? 3.610 3.770 ? 20.400 ? 11823 577 ? 577 100.000 ? ? ? ? 0.148 ? ? ? ? ? ? ? ? 20.490 ? ? ? ? 0.151 ? ? 9 1 0.999 ? ? ? ? ? ? ? ? ? ? 3.770 3.950 ? 24.030 ? 12452 570 ? 570 100.000 ? ? ? ? 0.135 ? ? ? ? ? ? ? ? 21.846 ? ? ? ? 0.138 ? ? 10 1 0.999 ? ? ? ? ? ? ? ? ? ? 3.950 4.170 ? 26.480 ? 11757 534 ? 534 100.000 ? ? ? ? 0.119 ? ? ? ? ? ? ? ? 22.017 ? ? ? ? 0.122 ? ? 11 1 0.999 ? ? ? ? ? ? ? ? ? ? 4.170 4.420 ? 25.690 ? 10852 497 ? 497 100.000 ? ? ? ? 0.125 ? ? ? ? ? ? ? ? 21.835 ? ? ? ? 0.128 ? ? 12 1 0.999 ? ? ? ? ? ? ? ? ? ? 4.420 4.720 ? 27.510 ? 10270 476 ? 476 100.000 ? ? ? ? 0.119 ? ? ? ? ? ? ? ? 21.576 ? ? ? ? 0.122 ? ? 13 1 0.999 ? ? ? ? ? ? ? ? ? ? 4.720 5.100 ? 24.360 ? 9014 443 ? 442 99.800 ? ? ? ? 0.136 ? ? ? ? ? ? ? ? 20.394 ? ? ? ? 0.140 ? ? 14 1 0.998 ? ? ? ? ? ? ? ? ? ? 5.100 5.590 ? 31.100 ? 8053 405 ? 405 100.000 ? ? ? ? 0.103 ? ? ? ? ? ? ? ? 19.884 ? ? ? ? 0.106 ? ? 15 1 0.999 ? ? ? ? ? ? ? ? ? ? 5.590 6.250 ? 37.350 ? 7728 359 ? 359 100.000 ? ? ? ? 0.087 ? ? ? ? ? ? ? ? 21.526 ? ? ? ? 0.089 ? ? 16 1 0.999 ? ? ? ? ? ? ? ? ? ? 6.250 7.220 ? 52.780 ? 7156 328 ? 328 100.000 ? ? ? ? 0.057 ? ? ? ? ? ? ? ? 21.817 ? ? ? ? 0.058 ? ? 17 1 1.000 ? ? ? ? ? ? ? ? ? ? 7.220 8.840 ? 65.590 ? 5677 272 ? 272 100.000 ? ? ? ? 0.040 ? ? ? ? ? ? ? ? 20.871 ? ? ? ? 0.041 ? ? 18 1 1.000 ? ? ? ? ? ? ? ? ? ? 8.840 12.500 ? 70.670 ? 4153 214 ? 214 100.000 ? ? ? ? 0.035 ? ? ? ? ? ? ? ? 19.407 ? ? ? ? 0.036 ? ? 19 1 1.000 ? ? ? ? ? ? ? ? ? ? 12.500 36.960 ? 86.290 ? 2512 119 ? 117 98.300 ? ? ? ? 0.026 ? ? ? ? ? ? ? ? 21.470 ? ? ? ? 0.027 ? ? 20 1 1.000 ? ? ? ? ? ? ? ? ? ? # _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 98.150 _refine.B_iso_mean 46.1664 _refine.B_iso_min 30.370 _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 7XKM _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 2.7900 _refine.ls_d_res_low 36.9600 _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 10274 _refine.ls_number_reflns_R_free 1037 _refine.ls_number_reflns_R_work 9237 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 99.7800 _refine.ls_percent_reflns_R_free 10.0900 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1901 _refine.ls_R_factor_R_free 0.2170 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1869 _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 1.360 _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 SAD _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 26.9000 _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 0.2400 _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 2.7900 _refine_hist.d_res_low 36.9600 _refine_hist.number_atoms_solvent 6 _refine_hist.number_atoms_total 985 _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 48 _refine_hist.pdbx_B_iso_mean_ligand 49.77 _refine_hist.pdbx_B_iso_mean_solvent 34.19 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 956 _refine_hist.pdbx_number_atoms_ligand 23 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # 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' 2.7900 2.9400 1450 . 144 1306 99.0000 . . . 0.2294 0.0000 0.1939 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 2.9400 3.1300 1473 . 144 1329 100.0000 . . . 0.2571 0.0000 0.1846 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 3.1300 3.3700 1484 . 153 1331 100.0000 . . . 0.2417 0.0000 0.1999 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 3.3700 3.7100 1452 . 153 1299 100.0000 . . . 0.2814 0.0000 0.1973 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 3.7100 4.2400 1478 . 153 1325 100.0000 . . . 0.1767 0.0000 0.1823 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 4.2400 5.3400 1461 . 140 1321 100.0000 . . . 0.2608 0.0000 0.2061 . . . . . . . 7 . . . 'X-RAY DIFFRACTION' 5.3400 36.9600 1476 . 150 1326 100.0000 . . . 0.1584 0.0000 0.1670 . . . . . . . 7 . . . # _struct.entry_id 7XKM _struct.title 'Crystal structure of DNA-Ag(I) rod comprising a one-dimensional array of 11 silver ions' _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 7XKM _struct_keywords.text 'DNA, Silver, Rod' _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 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 2 ? N N N 2 ? O N N 2 ? P N N 2 ? Q N N 2 ? R N N 2 ? S N N 2 ? T N N 2 ? U N N 2 ? V N N 2 ? W N N 2 ? X N N 2 ? Y N N 2 ? Z N N 2 ? AA N N 2 ? BA N N 3 ? CA N N 3 ? DA N N 3 ? EA N N 3 ? # 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 DC 5 "O3'" ? ? ? 1_555 A BRU 6 P ? ? A DC 5 A BRU 6 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale2 covale both ? A BRU 6 "O3'" ? ? ? 1_555 A DC 7 P ? ? A BRU 6 A DC 7 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale3 covale both ? A DC 7 "O3'" ? ? ? 1_555 A BRU 8 P ? ? A DC 7 A BRU 8 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale4 covale both ? A BRU 8 "O3'" ? ? ? 1_555 A DC 9 P ? ? A BRU 8 A DC 9 1_555 ? ? ? ? ? ? ? 1.610 ? ? covale5 covale both ? B DC 5 "O3'" ? ? ? 1_555 B BRU 6 P ? ? B DC 5 B BRU 6 1_555 ? ? ? ? ? ? ? 1.599 ? ? covale6 covale both ? B BRU 6 "O3'" ? ? ? 1_555 B DC 7 P ? ? B BRU 6 B DC 7 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale7 covale both ? B DC 7 "O3'" ? ? ? 1_555 B BRU 8 P ? ? B DC 7 B BRU 8 1_555 ? ? ? ? ? ? ? 1.607 ? ? covale8 covale both ? B BRU 8 "O3'" ? ? ? 1_555 B DC 9 P ? ? B BRU 8 B DC 9 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale9 covale both ? C DC 5 "O3'" ? ? ? 1_555 C BRU 6 P ? ? C DC 5 C BRU 6 1_555 ? ? ? ? ? ? ? 1.604 ? ? covale10 covale both ? C BRU 6 "O3'" ? ? ? 1_555 C DC 7 P ? ? C BRU 6 C DC 7 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale11 covale both ? C DC 7 "O3'" ? ? ? 1_555 C BRU 8 P ? ? C DC 7 C BRU 8 1_555 ? ? ? ? ? ? ? 1.601 ? ? covale12 covale both ? C BRU 8 "O3'" ? ? ? 1_555 C DC 9 P ? ? C BRU 8 C DC 9 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale13 covale both ? D DC 5 "O3'" ? ? ? 1_555 D BRU 6 P ? ? D DC 5 D BRU 6 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale14 covale both ? D BRU 6 "O3'" ? ? ? 1_555 D DC 7 P ? ? D BRU 6 D DC 7 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale15 covale both ? D DC 7 "O3'" ? ? ? 1_555 D BRU 8 P ? ? D DC 7 D BRU 8 1_555 ? ? ? ? ? ? ? 1.603 ? ? covale16 covale both ? D BRU 8 "O3'" ? ? ? 1_555 D DC 9 P ? ? D BRU 8 D DC 9 1_555 ? ? ? ? ? ? ? 1.606 ? ? metalc1 metalc ? ? A DC 1 N3 ? ? ? 1_555 N AG . AG ? ? A DC 1 B AG 101 1_555 ? ? ? ? ? ? ? 2.210 ? ? metalc2 metalc ? ? A DG 2 N7 ? ? ? 1_555 O AG . AG ? ? A DG 2 B AG 102 1_555 ? ? ? ? ? ? ? 2.183 ? ? metalc3 metalc ? ? A DC 3 N3 ? ? ? 1_555 E AG . AG ? ? A DC 3 A AG 101 1_555 ? ? ? ? ? ? ? 2.186 ? ? metalc4 metalc ? ? A DG 4 N7 ? ? ? 1_555 F AG . AG ? ? A DG 4 A AG 102 1_555 ? ? ? ? ? ? ? 2.241 ? ? metalc5 metalc ? ? A DC 5 N3 ? ? ? 1_555 P AG . AG ? ? A DC 5 B AG 103 1_555 ? ? ? ? ? ? ? 2.128 ? ? metalc6 metalc ? ? A BRU 6 N3 ? ? ? 1_555 G AG . AG ? ? A BRU 6 A AG 103 1_555 ? ? ? ? ? ? ? 1.918 ? ? metalc7 metalc ? ? A DC 7 N3 ? ? ? 1_555 H AG . AG ? ? A DC 7 A AG 104 1_555 ? ? ? ? ? ? ? 2.060 ? ? metalc8 metalc ? ? A BRU 8 N3 ? ? ? 1_555 I AG . AG ? ? A BRU 8 A AG 105 1_555 ? ? ? ? ? ? ? 1.948 ? ? metalc9 metalc ? ? A BRU 8 O2 ? ? ? 1_555 I AG . AG ? ? A BRU 8 A AG 105 1_555 ? ? ? ? ? ? ? 2.696 ? ? metalc10 metalc ? ? A DC 9 N3 ? ? ? 1_555 J AG . AG ? ? A DC 9 A AG 106 1_555 ? ? ? ? ? ? ? 2.023 ? ? metalc11 metalc ? ? A DG 10 N7 ? ? ? 1_555 K AG . AG ? ? A DG 10 A AG 107 1_555 ? ? ? ? ? ? ? 2.071 ? ? metalc12 metalc ? ? A DC 11 N3 ? ? ? 1_555 L AG . AG ? ? A DC 11 A AG 108 1_555 ? ? ? ? ? ? ? 2.101 ? ? metalc13 metalc ? ? E AG . AG ? ? ? 1_555 B DC 9 N3 ? ? A AG 101 B DC 9 1_555 ? ? ? ? ? ? ? 2.222 ? ? metalc14 metalc ? ? F AG . AG ? ? ? 1_555 B BRU 8 N3 ? ? A AG 102 B BRU 8 1_555 ? ? ? ? ? ? ? 1.919 ? ? metalc15 metalc ? ? G AG . AG ? ? ? 1_555 B BRU 6 N3 ? ? A AG 103 B BRU 6 1_555 ? ? ? ? ? ? ? 1.904 ? ? metalc16 metalc ? ? H AG . AG ? ? ? 1_555 B DC 5 N3 ? ? A AG 104 B DC 5 1_555 ? ? ? ? ? ? ? 2.038 ? ? metalc17 metalc ? ? I AG . AG ? ? ? 1_555 B DG 4 N7 ? ? A AG 105 B DG 4 1_555 ? ? ? ? ? ? ? 2.022 ? ? metalc18 metalc ? ? J AG . AG ? ? ? 1_555 B DC 3 N3 ? ? A AG 106 B DC 3 1_555 ? ? ? ? ? ? ? 2.100 ? ? metalc19 metalc ? ? K AG . AG ? ? ? 1_555 B DG 2 N7 ? ? A AG 107 B DG 2 1_555 ? ? ? ? ? ? ? 2.159 ? ? metalc20 metalc ? ? L AG . AG ? ? ? 1_555 B DC 1 N3 ? ? A AG 108 B DC 1 1_555 ? ? ? ? ? ? ? 2.114 ? ? metalc21 metalc ? ? B DC 7 N3 ? ? ? 1_555 P AG . AG ? ? B DC 7 B AG 103 1_555 ? ? ? ? ? ? ? 2.142 ? ? metalc22 metalc ? ? B DG 10 N7 ? ? ? 1_555 O AG . AG ? ? B DG 10 B AG 102 1_555 ? ? ? ? ? ? ? 2.002 ? ? metalc23 metalc ? ? B DC 11 N3 ? ? ? 1_555 N AG . AG ? ? B DC 11 B AG 101 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc24 metalc ? ? N AG . AG ? ? ? 12_666 D DG 12 O6 ? ? B AG 101 D DG 12 1_555 ? ? ? ? ? ? ? 2.680 ? ? metalc25 metalc ? ? C DC 1 N3 ? ? ? 1_555 AA AG . AG ? ? C DC 1 D AG 105 1_555 ? ? ? ? ? ? ? 2.052 ? ? metalc26 metalc ? ? C DG 2 N7 ? ? ? 1_555 V AG . AG ? ? C DG 2 C AG 106 1_555 ? ? ? ? ? ? ? 2.009 ? ? metalc27 metalc ? ? C DC 3 N3 ? ? ? 1_555 U AG . AG ? ? C DC 3 C AG 105 1_555 ? ? ? ? ? ? ? 2.296 ? ? metalc28 metalc ? ? C DG 4 N7 ? ? ? 1_555 Z AG . AG ? ? C DG 4 D AG 104 1_555 ? ? ? ? ? ? ? 2.141 ? ? metalc29 metalc ? ? C DC 5 N3 ? ? ? 1_555 Y AG . AG ? ? C DC 5 D AG 103 1_555 ? ? ? ? ? ? ? 2.010 ? ? metalc30 metalc ? ? C BRU 6 N3 ? ? ? 1_555 T AG . AG ? ? C BRU 6 C AG 104 1_555 ? ? ? ? ? ? ? 1.877 ? ? metalc31 metalc ? ? C DC 7 N3 ? ? ? 1_555 S AG . AG ? ? C DC 7 C AG 103 1_555 ? ? ? ? ? ? ? 2.153 ? ? metalc32 metalc ? ? C BRU 8 N3 ? ? ? 1_555 R AG . AG ? ? C BRU 8 C AG 102 1_555 ? ? ? ? ? ? ? 1.909 ? ? metalc33 metalc ? ? C DC 9 N3 ? ? ? 1_555 X AG . AG ? ? C DC 9 D AG 102 1_555 ? ? ? ? ? ? ? 1.984 ? ? metalc34 metalc ? ? C DG 10 N7 ? ? ? 1_555 W AG . AG ? ? C DG 10 D AG 101 1_555 ? ? ? ? ? ? ? 2.172 ? ? metalc35 metalc ? ? C DC 11 N3 ? ? ? 1_555 Q AG . AG ? ? C DC 11 C AG 101 1_555 ? ? ? ? ? ? ? 2.210 ? ? metalc36 metalc ? ? Q AG . AG ? ? ? 1_555 D DC 1 N3 ? ? C AG 101 D DC 1 1_555 ? ? ? ? ? ? ? 2.083 ? ? metalc37 metalc ? ? R AG . AG ? ? ? 1_555 D DG 4 N7 ? ? C AG 102 D DG 4 1_555 ? ? ? ? ? ? ? 2.166 ? ? metalc38 metalc ? ? S AG . AG ? ? ? 1_555 D DC 5 N3 ? ? C AG 103 D DC 5 1_555 ? ? ? ? ? ? ? 2.140 ? ? metalc39 metalc ? ? T AG . AG ? ? ? 1_555 D BRU 6 N3 ? ? C AG 104 D BRU 6 1_555 ? ? ? ? ? ? ? 1.939 ? ? metalc40 metalc ? ? U AG . AG ? ? ? 1_555 D DC 9 N3 ? ? C AG 105 D DC 9 1_555 ? ? ? ? ? ? ? 2.000 ? ? metalc41 metalc ? ? V AG . AG ? ? ? 1_555 D DG 10 N7 ? ? C AG 106 D DG 10 1_555 ? ? ? ? ? ? ? 2.053 ? ? metalc42 metalc ? ? D DG 2 N7 ? ? ? 1_555 W AG . AG ? ? D DG 2 D AG 101 1_555 ? ? ? ? ? ? ? 2.177 ? ? metalc43 metalc ? ? D DC 3 N3 ? ? ? 1_555 X AG . AG ? ? D DC 3 D AG 102 1_555 ? ? ? ? ? ? ? 2.137 ? ? metalc44 metalc ? ? D DC 7 N3 ? ? ? 1_555 Y AG . AG ? ? D DC 7 D AG 103 1_555 ? ? ? ? ? ? ? 1.998 ? ? metalc45 metalc ? ? D BRU 8 N3 ? ? ? 1_555 Z AG . AG ? ? D BRU 8 D AG 104 1_555 ? ? ? ? ? ? ? 1.947 ? ? metalc46 metalc ? ? D DC 11 N3 ? ? ? 1_555 AA AG . AG ? ? D DC 11 D AG 105 1_555 ? ? ? ? ? ? ? 2.076 ? ? hydrog1 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 1 B DG 10 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog2 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 2 B DC 9 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog3 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B BRU 8 O4 ? ? A DC 3 B BRU 8 1_555 ? ? ? ? ? ? 'DC-BRU MISPAIR' ? ? ? hydrog4 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 7 N4 ? ? A DG 4 B DC 7 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog5 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B BRU 6 O4 ? ? A DC 5 B BRU 6 1_555 ? ? ? ? ? ? 'DC-BRU MISPAIR' ? ? ? hydrog6 hydrog ? ? A BRU 6 O4 ? ? ? 1_555 B DC 5 N4 ? ? A BRU 6 B DC 5 1_555 ? ? ? ? ? ? 'BRU-DC MISPAIR' ? ? ? hydrog7 hydrog ? ? A DC 7 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 7 B DG 4 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog8 hydrog ? ? A BRU 8 O4 ? ? ? 1_555 B DC 3 N4 ? ? A BRU 8 B DC 3 1_555 ? ? ? ? ? ? 'BRU-DC MISPAIR' ? ? ? hydrog9 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 9 B DG 2 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog10 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 10 B DC 1 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog11 hydrog ? ? A DG 12 O6 ? ? ? 1_555 C DG 12 N1 ? ? A DG 12 C DG 12 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog12 hydrog ? ? C DC 1 N4 ? ? ? 1_555 D DG 10 O6 ? ? C DC 1 D DG 10 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog13 hydrog ? ? C DG 2 O6 ? ? ? 1_555 D DC 9 N4 ? ? C DG 2 D DC 9 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog14 hydrog ? ? C DC 3 N4 ? ? ? 1_555 D BRU 8 O4 ? ? C DC 3 D BRU 8 1_555 ? ? ? ? ? ? 'DC-BRU MISPAIR' ? ? ? hydrog15 hydrog ? ? C DG 4 O6 ? ? ? 1_555 D DC 7 N4 ? ? C DG 4 D DC 7 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog16 hydrog ? ? C DC 5 N4 ? ? ? 1_555 D BRU 6 O4 ? ? C DC 5 D BRU 6 1_555 ? ? ? ? ? ? 'DC-BRU MISPAIR' ? ? ? hydrog17 hydrog ? ? C BRU 6 O4 ? ? ? 1_555 D DC 5 N4 ? ? C BRU 6 D DC 5 1_555 ? ? ? ? ? ? 'BRU-DC MISPAIR' ? ? ? hydrog18 hydrog ? ? C DC 7 N4 ? ? ? 1_555 D DG 4 O6 ? ? C DC 7 D DG 4 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog19 hydrog ? ? C DC 9 N4 ? ? ? 1_555 D DG 2 O6 ? ? C DC 9 D DG 2 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog20 hydrog ? ? C DG 10 O6 ? ? ? 1_555 D DC 1 N4 ? ? C DG 10 D DC 1 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # _atom_sites.entry_id 7XKM _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] 0.012910 _atom_sites.fract_transf_matrix[1][2] 0.007453 _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] 0.014907 _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] 0.008083 _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 AG BR C N O P # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 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 BRU 6 6 6 BRU BRU A . n A 1 7 DC 7 7 7 DC DC A . n A 1 8 BRU 8 8 8 BRU BRU A . n A 1 9 DC 9 9 9 DC DC A . n A 1 10 DG 10 10 10 DG DG A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 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 BRU 6 6 6 BRU BRU B . n B 1 7 DC 7 7 7 DC DC B . n B 1 8 BRU 8 8 8 BRU BRU B . n B 1 9 DC 9 9 9 DC DC B . n B 1 10 DG 10 10 10 DG DG B . n B 1 11 DC 11 11 11 DC DC B . n B 1 12 DG 12 12 12 DG DG B . n C 1 1 DC 1 1 1 DC DC C . n C 1 2 DG 2 2 2 DG DG C . n C 1 3 DC 3 3 3 DC DC C . n C 1 4 DG 4 4 4 DG DG C . n C 1 5 DC 5 5 5 DC DC C . n C 1 6 BRU 6 6 6 BRU BRU C . n C 1 7 DC 7 7 7 DC DC C . n C 1 8 BRU 8 8 8 BRU BRU C . n C 1 9 DC 9 9 9 DC DC C . n C 1 10 DG 10 10 10 DG DG C . n C 1 11 DC 11 11 11 DC DC C . n C 1 12 DG 12 12 12 DG DG C . n D 1 1 DC 1 1 1 DC DC D . n D 1 2 DG 2 2 2 DG DG D . n D 1 3 DC 3 3 3 DC DC D . n D 1 4 DG 4 4 4 DG DG D . n D 1 5 DC 5 5 5 DC DC D . n D 1 6 BRU 6 6 6 BRU BRU D . n D 1 7 DC 7 7 7 DC DC D . n D 1 8 BRU 8 8 8 BRU BRU D . n D 1 9 DC 9 9 9 DC DC D . n D 1 10 DG 10 10 10 DG DG D . n D 1 11 DC 11 11 11 DC DC D . n D 1 12 DG 12 12 12 DG DG D . 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 # 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 E 2 AG 1 101 3 AG AG A . F 2 AG 1 102 4 AG AG A . G 2 AG 1 103 6 AG AG A . H 2 AG 1 104 7 AG AG A . I 2 AG 1 105 8 AG AG A . J 2 AG 1 106 9 AG AG A . K 2 AG 1 107 10 AG AG A . L 2 AG 1 108 11 AG AG A . M 2 AG 1 109 28 AG AG A . N 2 AG 1 101 1 AG AG B . O 2 AG 1 102 2 AG AG B . P 2 AG 1 103 5 AG AG B . Q 2 AG 1 101 12 AG AG C . R 2 AG 1 102 15 AG AG C . S 2 AG 1 103 16 AG AG C . T 2 AG 1 104 17 AG AG C . U 2 AG 1 105 20 AG AG C . V 2 AG 1 106 21 AG AG C . W 2 AG 1 101 13 AG AG D . X 2 AG 1 102 14 AG AG D . Y 2 AG 1 103 18 AG AG D . Z 2 AG 1 104 19 AG AG D . AA 2 AG 1 105 22 AG AG D . BA 3 HOH 1 201 19 HOH HOH A . BA 3 HOH 2 202 4 HOH HOH A . CA 3 HOH 1 201 6 HOH HOH B . DA 3 HOH 1 201 11 HOH HOH C . DA 3 HOH 2 202 18 HOH HOH C . EA 3 HOH 1 201 1 HOH HOH D . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 # _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA # 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)' 12380 ? 1 MORE -129 ? 1 'SSA (A^2)' 5190 ? # _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_ _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 DC 1 ? A DC 1 ? 1_555 AG ? N AG . ? B AG 101 ? 1_555 N3 ? B DC 11 ? B DC 11 ? 1_555 177.9 ? 2 N3 ? A DC 1 ? A DC 1 ? 1_555 AG ? N AG . ? B AG 101 ? 1_555 O6 ? D DG 12 ? D DG 12 ? 1_555 97.1 ? 3 N3 ? B DC 11 ? B DC 11 ? 1_555 AG ? N AG . ? B AG 101 ? 1_555 O6 ? D DG 12 ? D DG 12 ? 1_555 83.5 ? 4 N7 ? A DG 2 ? A DG 2 ? 1_555 AG ? O AG . ? B AG 102 ? 1_555 N7 ? B DG 10 ? B DG 10 ? 1_555 167.6 ? 5 N3 ? A DC 3 ? A DC 3 ? 1_555 AG ? E AG . ? A AG 101 ? 1_555 N3 ? B DC 9 ? B DC 9 ? 1_555 172.5 ? 6 N7 ? A DG 4 ? A DG 4 ? 1_555 AG ? F AG . ? A AG 102 ? 1_555 N3 ? B BRU 8 ? B BRU 8 ? 1_555 172.6 ? 7 N3 ? A DC 5 ? A DC 5 ? 1_555 AG ? P AG . ? B AG 103 ? 1_555 N3 ? B DC 7 ? B DC 7 ? 1_555 172.1 ? 8 N3 ? A BRU 6 ? A BRU 6 ? 1_555 AG ? G AG . ? A AG 103 ? 1_555 N3 ? B BRU 6 ? B BRU 6 ? 1_555 171.1 ? 9 N3 ? A DC 7 ? A DC 7 ? 1_555 AG ? H AG . ? A AG 104 ? 1_555 N3 ? B DC 5 ? B DC 5 ? 1_555 176.2 ? 10 N3 ? A BRU 8 ? A BRU 8 ? 1_555 AG ? I AG . ? A AG 105 ? 1_555 O2 ? A BRU 8 ? A BRU 8 ? 1_555 57.1 ? 11 N3 ? A BRU 8 ? A BRU 8 ? 1_555 AG ? I AG . ? A AG 105 ? 1_555 N7 ? B DG 4 ? B DG 4 ? 1_555 168.2 ? 12 O2 ? A BRU 8 ? A BRU 8 ? 1_555 AG ? I AG . ? A AG 105 ? 1_555 N7 ? B DG 4 ? B DG 4 ? 1_555 122.8 ? 13 N3 ? A DC 9 ? A DC 9 ? 1_555 AG ? J AG . ? A AG 106 ? 1_555 N3 ? B DC 3 ? B DC 3 ? 1_555 177.1 ? 14 N7 ? A DG 10 ? A DG 10 ? 1_555 AG ? K AG . ? A AG 107 ? 1_555 N7 ? B DG 2 ? B DG 2 ? 1_555 175.3 ? 15 N3 ? A DC 11 ? A DC 11 ? 1_555 AG ? L AG . ? A AG 108 ? 1_555 N3 ? B DC 1 ? B DC 1 ? 1_555 168.7 ? 16 N3 ? C DC 1 ? C DC 1 ? 1_555 AG ? AA AG . ? D AG 105 ? 1_555 N3 ? D DC 11 ? D DC 11 ? 1_555 175.1 ? 17 N7 ? C DG 2 ? C DG 2 ? 1_555 AG ? V AG . ? C AG 106 ? 1_555 N7 ? D DG 10 ? D DG 10 ? 1_555 163.6 ? 18 N3 ? C DC 3 ? C DC 3 ? 1_555 AG ? U AG . ? C AG 105 ? 1_555 N3 ? D DC 9 ? D DC 9 ? 1_555 173.8 ? 19 N7 ? C DG 4 ? C DG 4 ? 1_555 AG ? Z AG . ? D AG 104 ? 1_555 N3 ? D BRU 8 ? D BRU 8 ? 1_555 169.9 ? 20 N3 ? C DC 5 ? C DC 5 ? 1_555 AG ? Y AG . ? D AG 103 ? 1_555 N3 ? D DC 7 ? D DC 7 ? 1_555 169.6 ? 21 N3 ? C BRU 6 ? C BRU 6 ? 1_555 AG ? T AG . ? C AG 104 ? 1_555 N3 ? D BRU 6 ? D BRU 6 ? 1_555 167.2 ? 22 N3 ? C DC 7 ? C DC 7 ? 1_555 AG ? S AG . ? C AG 103 ? 1_555 N3 ? D DC 5 ? D DC 5 ? 1_555 175.7 ? 23 N3 ? C BRU 8 ? C BRU 8 ? 1_555 AG ? R AG . ? C AG 102 ? 1_555 N7 ? D DG 4 ? D DG 4 ? 1_555 170.5 ? 24 N3 ? C DC 9 ? C DC 9 ? 1_555 AG ? X AG . ? D AG 102 ? 1_555 N3 ? D DC 3 ? D DC 3 ? 1_555 177.0 ? 25 N7 ? C DG 10 ? C DG 10 ? 1_555 AG ? W AG . ? D AG 101 ? 1_555 N7 ? D DG 2 ? D DG 2 ? 1_555 170.2 ? 26 N3 ? C DC 11 ? C DC 11 ? 1_555 AG ? Q AG . ? C AG 101 ? 1_555 N3 ? D DC 1 ? D DC 1 ? 1_555 164.9 ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2022-07-06 2 'Structure model' 1 1 2022-08-10 3 'Structure model' 1 2 2022-10-19 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 3 'Structure model' citation_author # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.identifier_ORCID' 5 3 'Structure model' '_citation.page_first' 6 3 'Structure model' '_citation.page_last' 7 3 'Structure model' '_citation_author.identifier_ORCID' # 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 reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 # _pdbx_entry_details.entry_id 7XKM _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.29 108.30 2.99 0.30 N 2 1 "O4'" A DC 7 ? ? "C1'" A DC 7 ? ? N1 A DC 7 ? ? 110.74 108.30 2.44 0.30 N 3 1 "O4'" B DG 2 ? ? "C1'" B DG 2 ? ? N9 B DG 2 ? ? 110.40 108.30 2.10 0.30 N 4 1 "O4'" B DC 3 ? ? "C4'" B DC 3 ? ? "C3'" B DC 3 ? ? 101.89 104.50 -2.61 0.40 N 5 1 "O4'" B DC 3 ? ? "C1'" B DC 3 ? ? N1 B DC 3 ? ? 110.20 108.30 1.90 0.30 N 6 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 110.18 108.30 1.88 0.30 N 7 1 "O4'" B DG 10 ? ? "C1'" B DG 10 ? ? N9 B DG 10 ? ? 110.45 108.30 2.15 0.30 N 8 1 "O4'" C DG 2 ? ? "C1'" C DG 2 ? ? N9 C DG 2 ? ? 110.60 108.30 2.30 0.30 N 9 1 "O4'" C DG 4 ? ? "C1'" C DG 4 ? ? N9 C DG 4 ? ? 110.56 108.30 2.26 0.30 N 10 1 "O4'" D DG 2 ? ? "C1'" D DG 2 ? ? N9 D DG 2 ? ? 110.80 108.30 2.50 0.30 N # _ndb_struct_conf_na.entry_id 7XKM _ndb_struct_conf_na.feature '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 10 1_555 0.190 3.149 -0.358 -33.908 -15.231 -113.701 1 A_DC1:DG10_B A 1 ? B 10 ? ? ? 1 A DG 2 1_555 B DC 9 1_555 0.069 -3.520 0.999 25.529 16.407 121.025 2 A_DG2:DC9_B A 2 ? B 9 ? ? ? 1 A DC 3 1_555 B BRU 8 1_555 0.473 -0.651 -2.199 -1.707 -28.696 -24.653 3 A_DC3:BRU8_B A 3 ? B 8 ? ? ? 1 A DG 4 1_555 B DC 7 1_555 -0.426 -2.961 0.767 30.513 18.035 110.029 4 A_DG4:DC7_B A 4 ? B 7 ? ? ? 1 A DC 5 1_555 B BRU 6 1_555 0.203 -0.553 -1.846 2.386 -42.390 -20.149 5 A_DC5:BRU6_B A 5 ? B 6 ? ? ? 1 A BRU 6 1_555 B DC 5 1_555 -0.362 -0.614 -2.070 3.412 -37.496 -22.103 6 A_BRU6:DC5_B A 6 ? B 5 ? ? ? 1 A DC 7 1_555 B DG 4 1_555 -0.210 3.015 -1.103 -22.706 -33.015 -114.421 7 A_DC7:DG4_B A 7 ? B 4 ? ? ? 1 A BRU 8 1_555 B DC 3 1_555 -0.687 -0.485 -1.742 6.186 -37.898 -19.405 8 A_BRU8:DC3_B A 8 ? B 3 ? ? ? 1 A DC 9 1_555 B DG 2 1_555 -0.127 3.515 -0.652 -30.243 -29.061 -109.483 9 A_DC9:DG2_B A 9 ? B 2 ? ? ? 1 A DG 10 1_555 B DC 1 1_555 0.195 -3.416 0.550 27.580 10.482 124.178 10 A_DG10:DC1_B A 10 ? B 1 ? ? ? 1 A DG 12 1_555 C DG 12 1_555 -1.900 1.118 -1.237 10.873 -43.549 -10.813 11 A_DG12:DG12_C A 12 ? C 12 ? ? 1 1 D DC 1 1_555 C DG 10 1_555 -0.487 3.942 -0.669 -26.142 -21.102 -126.931 12 D_DC1:DG10_C D 1 ? C 10 ? ? ? 1 D DG 2 1_555 C DC 9 1_555 0.392 -3.412 0.343 29.863 20.952 123.852 13 D_DG2:DC9_C D 2 ? C 9 ? ? ? 1 C DC 7 1_555 D DG 4 1_555 0.029 3.078 -0.902 -27.721 -21.831 -113.519 14 C_DC7:DG4_D C 7 ? D 4 ? ? ? 1 C BRU 6 1_555 D DC 5 1_555 -0.368 -0.551 -1.828 -3.816 -37.807 -15.575 15 C_BRU6:DC5_D C 6 ? D 5 ? ? ? 1 D BRU 6 1_555 C DC 5 1_555 -0.239 -0.359 -2.230 -4.970 -49.582 -29.731 16 D_BRU6:DC5_C D 6 ? C 5 ? ? ? 1 D DC 7 1_555 C DG 4 1_555 0.014 3.246 -0.953 -29.096 -27.546 -111.387 17 D_DC7:DG4_C D 7 ? C 4 ? ? ? 1 D BRU 8 1_555 C DC 3 1_555 -1.284 -0.158 -1.967 12.625 -34.547 -24.566 18 D_BRU8:DC3_C D 8 ? C 3 ? ? ? 1 D DC 9 1_555 C DG 2 1_555 -0.292 3.073 -0.883 -28.265 -16.505 -122.367 19 D_DC9:DG2_C D 9 ? C 2 ? ? ? 1 D DG 10 1_555 C DC 1 1_555 0.101 -3.129 0.669 33.404 22.070 117.353 20 D_DG10:DC1_C D 10 ? C 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 10 1_555 A DG 2 1_555 B DC 9 1_555 -3.981 -1.593 1.359 -154.344 88.524 -117.994 0.717 -2.129 -0.206 -44.336 -77.300 -178.933 1 AA_DC1DG2:DC9DG10_BB A 1 ? B 10 ? A 2 ? B 9 ? 1 A DG 2 1_555 B DC 9 1_555 A DC 3 1_555 B BRU 8 1_555 1.808 2.224 1.765 -122.210 116.857 72.158 0.589 -1.457 1.229 59.974 62.722 171.186 2 AA_DG2DC3:BRU8DC9_BB A 2 ? B 9 ? A 3 ? B 8 ? 1 A DC 3 1_555 B BRU 8 1_555 A DG 4 1_555 B DC 7 1_555 -1.377 3.388 -1.442 176.472 -24.458 -137.703 -1.721 -0.885 -0.685 12.238 88.297 -179.336 3 AA_DC3DG4:DC7BRU8_BB A 3 ? B 8 ? A 4 ? B 7 ? 1 A DG 4 1_555 B DC 7 1_555 A DC 5 1_555 B BRU 6 1_555 -2.866 -0.867 -1.668 128.991 -121.692 -0.897 0.368 -1.502 1.477 61.753 65.457 -177.335 4 AA_DG4DC5:BRU6DC7_BB A 4 ? B 7 ? A 5 ? B 6 ? 1 A DC 5 1_555 B BRU 6 1_555 A BRU 6 1_555 B DC 5 1_555 -0.143 -0.016 2.793 1.019 -0.813 39.409 0.058 0.314 2.789 -1.205 -1.510 39.430 5 AA_DC5BRU6:DC5BRU6_BB A 5 ? B 6 ? A 6 ? B 5 ? 1 A BRU 6 1_555 B DC 5 1_555 A DC 7 1_555 B DG 4 1_555 1.365 -1.588 2.400 1.165 2.400 81.246 -1.264 -1.026 2.377 1.843 -0.894 81.282 6 AA_BRU6DC7:DG4DC5_BB A 6 ? B 5 ? A 7 ? B 4 ? 1 A DC 7 1_555 B DG 4 1_555 A BRU 8 1_555 B DC 3 1_555 -0.426 2.058 3.402 -2.473 2.570 -12.812 -11.513 -4.365 2.803 -11.235 -10.811 -13.297 7 AA_DC7BRU8:DC3DG4_BB A 7 ? B 4 ? A 8 ? B 3 ? 1 A BRU 8 1_555 B DC 3 1_555 A DC 9 1_555 B DG 2 1_555 1.457 -1.619 2.411 1.065 -3.530 89.561 -1.095 -1.017 2.474 -2.505 -0.756 89.620 8 AA_BRU8DC9:DG2DC3_BB A 8 ? B 3 ? A 9 ? B 2 ? 1 A DC 9 1_555 B DG 2 1_555 A DG 10 1_555 B DC 1 1_555 1.408 3.453 -3.042 154.913 -87.445 -11.004 -2.367 -0.429 0.177 44.191 78.287 -177.899 9 AA_DC9DG10:DC1DG2_BB A 9 ? B 2 ? A 10 ? B 1 ? 1 A DG 10 1_555 B DC 1 1_555 A DG 12 1_555 C DG 12 1_555 0.405 4.894 0.640 -107.657 119.398 -55.158 -2.015 0.619 -2.673 -63.510 -57.265 -162.970 10 AA_DG10DG12:DG12DC1_CB A 10 ? B 1 ? A 12 ? C 12 ? 1 A DG 12 1_555 C DG 12 1_555 D DC 1 1_555 C DG 10 1_555 3.888 -1.249 4.037 -13.259 2.281 112.152 -0.781 -2.516 3.707 1.372 7.973 112.682 11 AD_DG12DC1:DG10DG12_CC A 12 ? C 12 ? D 1 ? C 10 ? 1 D DC 1 1_555 C DG 10 1_555 D DG 2 1_555 C DC 9 1_555 1.305 3.609 -2.698 159.280 -82.147 -18.567 -2.320 -0.346 0.053 41.224 79.932 -179.226 12 DD_DC1DG2:DC9DG10_CC D 1 ? C 10 ? D 2 ? C 9 ? 1 D DG 2 1_555 C DC 9 1_555 C DC 7 1_555 D DG 4 1_555 -1.769 0.255 -5.845 7.820 2.148 -72.136 -0.091 -1.949 -5.660 -1.819 6.620 -72.529 13 DC_DG2DC7:DG4DC9_DC D 2 ? C 9 ? C 7 ? D 4 ? 1 C DC 7 1_555 D DG 4 1_555 C BRU 6 1_555 D DC 5 1_555 -1.250 1.355 -2.326 -2.883 -2.828 -85.064 -1.048 -0.877 -2.322 2.090 -2.131 -85.142 14 CC_DC7BRU6:DC5DG4_DD C 7 ? D 4 ? C 6 ? D 5 ? 1 C BRU 6 1_555 D DC 5 1_555 D BRU 6 1_555 C DC 5 1_555 -1.136 -2.938 -0.587 167.539 -54.867 99.846 -1.534 0.370 -0.556 -27.569 -84.183 177.615 15 CD_BRU6BRU6:DC5DC5_CD C 6 ? D 5 ? D 6 ? C 5 ? 1 D BRU 6 1_555 C DC 5 1_555 D DC 7 1_555 C DG 4 1_555 1.503 -1.873 2.174 1.918 0.701 86.838 -1.372 -1.065 2.188 0.510 -1.395 86.858 16 DD_BRU6DC7:DG4DC5_CC D 6 ? C 5 ? D 7 ? C 4 ? 1 D DC 7 1_555 C DG 4 1_555 D BRU 8 1_555 C DC 3 1_555 -0.617 1.928 2.953 -2.130 -0.259 -20.161 -5.372 -2.619 2.897 0.736 -6.061 -20.274 17 DD_DC7BRU8:DC3DG4_CC D 7 ? C 4 ? D 8 ? C 3 ? 1 D BRU 8 1_555 C DC 3 1_555 D DC 9 1_555 C DG 2 1_555 1.289 -1.602 3.033 -1.128 -2.710 93.852 -1.050 -0.901 3.056 -1.854 0.772 93.888 18 DD_BRU8DC9:DG2DC3_CC D 8 ? C 3 ? D 9 ? C 2 ? 1 D DC 9 1_555 C DG 2 1_555 D DG 10 1_555 C DC 1 1_555 -0.824 4.434 -0.412 151.216 -87.409 -169.358 -2.223 -0.423 -0.138 43.710 75.618 -179.505 19 DD_DC9DG10:DC1DG2_CC D 9 ? C 2 ? D 10 ? C 1 ? # _pdbx_audit_support.funding_organization 'Japan Society for the Promotion of Science (JSPS)' _pdbx_audit_support.country Japan _pdbx_audit_support.grant_number 17H03033 _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id AG _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id AG _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 ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SILVER ION' AG 3 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'mass spectrometry' _pdbx_struct_assembly_auth_evidence.details ? #