data_7XLV # _entry.id 7XLV # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.380 _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 7XLV pdb_00007xlv 10.2210/pdb7xlv/pdb WWPDB D_1300029134 ? ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7XLV _pdbx_database_status.recvd_initial_deposition_date 2022-04-23 _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 'Cerretani, C.' 2 ? 'Vosch, 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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nanoscale Adv' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2516-0230 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 4 _citation.language ? _citation.page_first 3212 _citation.page_last 3217 _citation.title 'The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster.' _citation.year 2022 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1039/d2na00325b _citation.pdbx_database_id_PubMed 36132821 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cerretani, C.' 1 0000-0002-3048-5438 primary 'Liisberg, M.B.' 2 0000-0001-7623-5453 primary 'Ruck, V.' 3 0000-0002-7403-3118 primary 'Kondo, J.' 4 0000-0002-5682-3685 primary 'Vosch, T.' 5 0000-0001-5435-2181 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 90.000 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 7XLV _cell.details ? _cell.formula_units_Z ? _cell.length_a 24.212 _cell.length_a_esd ? _cell.length_b 41.474 _cell.length_b_esd ? _cell.length_c 45.301 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 8 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XLV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' _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*AP*CP*CP*TP*AP*IP*CP*GP*A)-3') ; 2998.980 2 ? ? ? ? 2 non-polymer syn '(4S)-2-METHYL-2,4-PENTANEDIOL' 118.174 1 ? ? ? ? 3 non-polymer syn 'SILVER ION' 107.868 19 ? ? ? ? 4 water nat water 18.015 57 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DA)(DC)(DC)(DT)(DA)(DI)(DC)(DG)(DA)' _entity_poly.pdbx_seq_one_letter_code_can CACCTAICGA _entity_poly.pdbx_strand_id A,B _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 DA n 1 3 DC n 1 4 DC n 1 5 DT n 1 6 DA n 1 7 DI n 1 8 DC n 1 9 DG n 1 10 DA 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 10 _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 7XLV _struct_ref.pdbx_db_accession 7XLV _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 7XLV A 1 ? 10 ? 7XLV 1 ? 10 ? 1 10 2 1 7XLV B 1 ? 10 ? 7XLV 1 ? 10 ? 1 10 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight AG non-polymer . 'SILVER ION' ? 'Ag 1' 107.868 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 DI 'DNA linking' y "2'-DEOXYINOSINE-5'-MONOPHOSPHATE" ? 'C10 H13 N4 O7 P' 332.207 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 MPD non-polymer . '(4S)-2-METHYL-2,4-PENTANEDIOL' ? 'C6 H14 O2' 118.174 # _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 7XLV _exptl.crystals_number 1 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # _exptl_crystal.colour ? _exptl_crystal.density_diffrn ? _exptl_crystal.density_Matthews 1.90 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 35.13 _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_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, lithium chloride, 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 EIGER X 16M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2022-02-23 _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 0.98 _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-17A' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.98 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline BL-17A _diffrn_source.pdbx_synchrotron_site 'Photon Factory' # _reflns.B_iso_Wilson_estimate 9.379 _reflns.entry_id 7XLV _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.100 _reflns.d_resolution_low 30.590 _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 35080 _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 97.500 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.428 _reflns.pdbx_Rmerge_I_obs 0.084 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 9.850 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.011 _reflns.pdbx_scaling_rejects 4 _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 0.100 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all 120254 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.995 _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 ? # 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 1.100 1.130 ? 3.000 ? 7785 2644 ? 2509 94.900 ? ? ? ? 0.397 ? ? ? ? ? ? ? ? 3.103 ? ? ? ? 0.477 ? ? 1 1 0.828 ? ? ? ? ? ? ? ? ? ? 1.130 1.160 ? 3.780 ? 8100 2629 ? 2500 95.100 ? ? ? ? 0.321 ? ? ? ? ? ? ? ? 3.240 ? ? ? ? 0.381 ? ? 2 1 0.894 ? ? ? ? ? ? ? ? ? ? 1.160 1.190 ? 5.060 ? 8599 2512 ? 2428 96.700 ? ? ? ? 0.248 ? ? ? ? ? ? ? ? 3.542 ? ? ? ? 0.291 ? ? 3 1 0.941 ? ? ? ? ? ? ? ? ? ? 1.190 1.230 ? 6.050 ? 8309 2447 ? 2366 96.700 ? ? ? ? 0.203 ? ? ? ? ? ? ? ? 3.512 ? ? ? ? 0.239 ? ? 4 1 0.961 ? ? ? ? ? ? ? ? ? ? 1.230 1.270 ? 6.860 ? 7980 2391 ? 2298 96.100 ? ? ? ? 0.171 ? ? ? ? ? ? ? ? 3.473 ? ? ? ? 0.201 ? ? 5 1 0.973 ? ? ? ? ? ? ? ? ? ? 1.270 1.310 ? 7.780 ? 7645 2251 ? 2221 98.700 ? ? ? ? 0.146 ? ? ? ? ? ? ? ? 3.442 ? ? ? ? 0.173 ? ? 6 1 0.976 ? ? ? ? ? ? ? ? ? ? 1.310 1.360 ? 8.370 ? 7270 2230 ? 2144 96.100 ? ? ? ? 0.135 ? ? ? ? ? ? ? ? 3.391 ? ? ? ? 0.160 ? ? 7 1 0.979 ? ? ? ? ? ? ? ? ? ? 1.360 1.420 ? 8.190 ? 6728 2159 ? 2097 97.100 ? ? ? ? 0.130 ? ? ? ? ? ? ? ? 3.208 ? ? ? ? 0.156 ? ? 8 1 0.980 ? ? ? ? ? ? ? ? ? ? 1.420 1.480 ? 8.430 ? 6150 2018 ? 1968 97.500 ? ? ? ? 0.118 ? ? ? ? ? ? ? ? 3.125 ? ? ? ? 0.142 ? ? 9 1 0.986 ? ? ? ? ? ? ? ? ? ? 1.480 1.550 ? 10.070 ? 7005 1961 ? 1921 98.000 ? ? ? ? 0.109 ? ? ? ? ? ? ? ? 3.647 ? ? ? ? 0.127 ? ? 10 1 0.991 ? ? ? ? ? ? ? ? ? ? 1.550 1.640 ? 10.950 ? 6674 1861 ? 1835 98.600 ? ? ? ? 0.101 ? ? ? ? ? ? ? ? 3.637 ? ? ? ? 0.118 ? ? 11 1 0.992 ? ? ? ? ? ? ? ? ? ? 1.640 1.740 ? 11.920 ? 6406 1793 ? 1779 99.200 ? ? ? ? 0.093 ? ? ? ? ? ? ? ? 3.601 ? ? ? ? 0.109 ? ? 12 1 0.991 ? ? ? ? ? ? ? ? ? ? 1.740 1.860 ? 13.740 ? 5817 1629 ? 1626 99.800 ? ? ? ? 0.079 ? ? ? ? ? ? ? ? 3.577 ? ? ? ? 0.093 ? ? 13 1 0.991 ? ? ? ? ? ? ? ? ? ? 1.860 2.000 ? 15.620 ? 5424 1540 ? 1532 99.500 ? ? ? ? 0.069 ? ? ? ? ? ? ? ? 3.540 ? ? ? ? 0.082 ? ? 14 1 0.992 ? ? ? ? ? ? ? ? ? ? 2.000 2.200 ? 17.370 ? 4849 1422 ? 1417 99.600 ? ? ? ? 0.059 ? ? ? ? ? ? ? ? 3.422 ? ? ? ? 0.070 ? ? 15 1 0.994 ? ? ? ? ? ? ? ? ? ? 2.200 2.460 ? 17.890 ? 3949 1277 ? 1256 98.400 ? ? ? ? 0.054 ? ? ? ? ? ? ? ? 3.144 ? ? ? ? 0.066 ? ? 16 1 0.990 ? ? ? ? ? ? ? ? ? ? 2.460 2.840 ? 19.270 ? 3738 1110 ? 1096 98.700 ? ? ? ? 0.053 ? ? ? ? ? ? ? ? 3.411 ? ? ? ? 0.063 ? ? 17 1 0.992 ? ? ? ? ? ? ? ? ? ? 2.840 3.470 ? 19.490 ? 3623 967 ? 965 99.800 ? ? ? ? 0.057 ? ? ? ? ? ? ? ? 3.754 ? ? ? ? 0.067 ? ? 18 1 0.994 ? ? ? ? ? ? ? ? ? ? 3.470 4.910 ? 20.960 ? 2772 729 ? 729 100.000 ? ? ? ? 0.055 ? ? ? ? ? ? ? ? 3.802 ? ? ? ? 0.064 ? ? 19 1 0.992 ? ? ? ? ? ? ? ? ? ? 4.910 30.590 ? 20.310 ? 1431 399 ? 393 98.500 ? ? ? ? 0.051 ? ? ? ? ? ? ? ? 3.641 ? ? ? ? 0.061 ? ? 20 1 0.995 ? ? ? ? ? ? ? ? ? ? # _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 24.350 _refine.B_iso_mean 12.0448 _refine.B_iso_min 6.130 _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 7XLV _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_abs_structure_details ? _refine.ls_abs_structure_Flack ? _refine.ls_abs_structure_Flack_esd ? _refine.ls_abs_structure_Rogers ? _refine.ls_abs_structure_Rogers_esd ? _refine.ls_d_res_high 1.1000 _refine.ls_d_res_low 30.5900 _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 35042 _refine.ls_number_reflns_R_free 1873 _refine.ls_number_reflns_R_work 31527 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.3500 _refine.ls_percent_reflns_R_free 10.0300 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1030 _refine.ls_R_factor_R_free 0.1098 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1022 _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 1.380 _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 6JR4 _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 8.8100 _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 0.0700 _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 1.1000 _refine_hist.d_res_low 30.5900 _refine_hist.number_atoms_solvent 59 _refine_hist.number_atoms_total 498 _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 20 _refine_hist.pdbx_B_iso_mean_ligand 11.65 _refine_hist.pdbx_B_iso_mean_solvent 18.31 _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 398 _refine_hist.pdbx_number_atoms_ligand 41 _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' 1.1000 1.1100 1343 . 132 1211 93.0000 . . . 0.2006 0.0000 0.1936 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.1100 1.1300 1353 . 135 1218 95.0000 . . . 0.1826 0.0000 0.1930 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.1300 1.1500 1369 . 139 1230 94.0000 . . . 0.1753 0.0000 0.1840 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.1500 1.1600 1395 . 136 1259 97.0000 . . . 0.1345 0.0000 0.1484 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.1600 1.1800 1401 . 140 1261 97.0000 . . . 0.1282 0.0000 0.1316 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.1800 1.2000 1380 . 142 1238 94.0000 . . . 0.1447 0.0000 0.1247 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.2000 1.2200 1393 . 139 1254 98.0000 . . . 0.1305 0.0000 0.1181 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.2200 1.2500 1397 . 139 1258 98.0000 . . . 0.1302 0.0000 0.1113 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.2500 1.2700 1360 . 137 1223 94.0000 . . . 0.1116 0.0000 0.1077 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.2700 1.3000 1431 . 143 1288 100.0000 . . . 0.1047 0.0000 0.1033 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.3000 1.3300 1405 . 141 1264 96.0000 . . . 0.1076 0.0000 0.0996 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.3300 1.3700 1379 . 140 1239 97.0000 . . . 0.1002 0.0000 0.0957 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.3700 1.4000 1415 . 142 1273 99.0000 . . . 0.0993 0.0000 0.1066 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.4000 1.4400 1363 . 142 1221 95.0000 . . . 0.0881 0.0000 0.1047 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.4400 1.4900 1412 . 134 1278 98.0000 . . . 0.1012 0.0000 0.0984 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.4900 1.5400 1389 . 143 1246 96.0000 . . . 0.1052 0.0000 0.0988 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.5400 1.6000 1453 . 145 1308 99.0000 . . . 0.1215 0.0000 0.1025 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.6100 1.6800 1395 . 136 1259 99.0000 . . . 0.0982 0.0000 0.1011 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.6800 1.7700 1429 . 141 1288 99.0000 . . . 0.0996 0.0000 0.0943 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.7700 1.8800 1442 . 144 1298 100.0000 . . . 0.1199 0.0000 0.0915 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 1.8800 2.0200 1423 . 144 1279 100.0000 . . . 0.0931 0.0000 0.0818 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 2.0200 2.2300 1437 . 146 1291 100.0000 . . . 0.0732 0.0000 0.0665 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 2.2300 2.5500 1410 . 143 1267 98.0000 . . . 0.0739 0.0000 0.0713 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 2.5500 3.2100 1446 . 147 1299 100.0000 . . . 0.1244 0.0000 0.0971 . . . . . . . 25 . . . 'X-RAY DIFFRACTION' 3.2100 30.5900 1422 . 145 1277 99.0000 . . . 0.1316 0.0000 0.1200 . . . . . . . 25 . . . # _struct.entry_id 7XLV _struct.title 'Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (G7I mutant)' _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 7XLV _struct_keywords.text 'Silver, nanocluster, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 3 ? K N N 3 ? L N N 3 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 3 ? Q N N 3 ? R N N 3 ? S N N 3 ? T N N 3 ? U N N 3 ? V N N 3 ? W N N 4 ? X N N 4 ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DC 1 O2 ? ? ? 1_555 D AG . AG ? ? A DC 1 A AG 102 1_555 ? ? ? ? ? ? ? 2.470 ? ? metalc2 metalc ? ? A DC 1 N3 ? ? ? 1_555 H AG . AG ? ? A DC 1 A AG 106 1_555 ? ? ? ? ? ? ? 2.294 ? ? metalc3 metalc ? ? A DC 3 N3 ? ? ? 1_555 D AG . AG ? ? A DC 3 A AG 102 1_555 ? ? ? ? ? ? ? 2.309 ? ? metalc4 metalc ? ? A DC 4 N3 ? ? ? 1_555 E AG . AG ? ? A DC 4 A AG 103 1_555 ? ? ? ? ? ? ? 2.384 ? ? metalc5 metalc ? ? A DC 4 O2 ? ? ? 1_555 N AG . AG ? ? A DC 4 B AG 102 1_555 ? ? ? ? ? ? ? 2.454 ? ? metalc6 metalc ? ? A DC 4 O2 ? ? ? 1_555 O AG . AG ? ? A DC 4 B AG 103 1_555 ? ? ? ? ? ? ? 2.689 ? ? metalc7 metalc ? ? A DA 6 OP1 ? ? ? 1_555 G AG . AG ? ? A DA 6 A AG 105 1_555 ? ? ? ? ? ? ? 2.368 ? ? metalc8 metalc ? ? A DA 6 N7 ? ? ? 1_555 K AG . AG ? ? A DA 6 A AG 109 1_555 ? ? ? ? ? ? ? 2.261 ? ? metalc9 metalc ? ? A DA 6 OP2 ? ? ? 1_555 P AG . AG ? ? A DA 6 B AG 104 1_555 ? ? ? ? ? ? ? 2.359 ? ? metalc10 metalc ? ? A DI 7 N7 ? ? ? 1_555 G AG . AG ? ? A DI 7 A AG 105 1_555 ? ? ? ? ? ? ? 2.365 ? ? metalc11 metalc ? ? A DI 7 O6 ? ? ? 1_555 J AG . AG ? ? A DI 7 A AG 108 1_555 ? ? ? ? ? ? ? 2.578 ? ? metalc12 metalc ? ? A DI 7 O6 ? ? ? 1_555 K AG . AG ? ? A DI 7 A AG 109 1_555 ? ? ? ? ? ? ? 2.526 ? ? metalc13 metalc ? ? A DC 8 N3 ? ? ? 1_555 F AG . AG ? ? A DC 8 A AG 104 1_555 ? ? ? ? ? ? ? 2.262 ? ? metalc14 metalc ? ? A DC 8 O2 ? ? ? 1_555 J AG . AG ? ? A DC 8 A AG 108 1_555 ? ? ? ? ? ? ? 2.667 ? ? metalc15 metalc ? ? A DG 9 O6 ? ? ? 1_555 E AG . AG ? ? A DG 9 A AG 103 1_555 ? ? ? ? ? ? ? 2.389 ? ? metalc16 metalc ? ? A DG 9 N1 ? ? ? 1_555 I AG . AG ? ? A DG 9 A AG 107 1_555 ? ? ? ? ? ? ? 2.268 ? ? metalc17 metalc ? ? D AG . AG ? ? ? 1_555 B DA 2 N1 ? ? A AG 102 B DA 2 1_555 ? ? ? ? ? ? ? 2.411 ? ? metalc18 metalc ? ? H AG . AG ? ? ? 1_555 B DC 3 O2 ? ? A AG 106 B DC 3 1_555 ? ? ? ? ? ? ? 2.634 ? ? metalc19 metalc ? ? H AG . AG ? ? ? 1_555 B DC 4 O2 ? ? A AG 106 B DC 4 1_555 ? ? ? ? ? ? ? 2.491 ? ? metalc20 metalc ? ? I AG . AG ? ? ? 1_555 B DC 4 O2 ? ? A AG 107 B DC 4 1_555 ? ? ? ? ? ? ? 2.540 ? ? metalc21 metalc ? ? K AG . AG ? ? ? 1_555 B DA 6 OP2 ? ? A AG 109 B DA 6 1_555 ? ? ? ? ? ? ? 2.327 ? ? metalc22 metalc ? ? B DC 1 O2 ? ? ? 1_555 M AG . AG ? ? B DC 1 B AG 101 1_555 ? ? ? ? ? ? ? 2.401 ? ? metalc23 metalc ? ? B DC 1 N3 ? ? ? 1_555 N AG . AG ? ? B DC 1 B AG 102 1_555 ? ? ? ? ? ? ? 2.281 ? ? metalc24 metalc ? ? B DC 3 N3 ? ? ? 1_555 M AG . AG ? ? B DC 3 B AG 101 1_555 ? ? ? ? ? ? ? 2.247 ? ? metalc25 metalc ? ? B DC 4 N3 ? ? ? 1_555 Q AG . AG ? ? B DC 4 B AG 105 1_555 ? ? ? ? ? ? ? 2.383 ? ? metalc26 metalc ? ? B DA 6 N7 ? ? ? 1_555 P AG . AG ? ? B DA 6 B AG 104 1_555 ? ? ? ? ? ? ? 2.289 ? ? metalc27 metalc ? ? B DA 6 OP1 ? ? ? 1_555 S AG . AG ? ? B DA 6 B AG 107 1_555 ? ? ? ? ? ? ? 2.345 ? ? metalc28 metalc ? ? B DI 7 O6 ? ? ? 1_555 P AG . AG ? ? B DI 7 B AG 104 1_555 ? ? ? ? ? ? ? 2.589 ? ? metalc29 metalc ? ? B DI 7 N7 ? ? ? 1_555 S AG . AG ? ? B DI 7 B AG 107 1_555 ? ? ? ? ? ? ? 2.361 ? ? metalc30 metalc ? ? B DI 7 O6 ? ? ? 1_555 T AG . AG ? ? B DI 7 B AG 108 1_555 ? ? ? ? ? ? ? 2.454 ? ? metalc31 metalc ? ? B DI 7 N1 ? ? ? 1_555 V AG . AG ? ? B DI 7 B AG 110 1_555 ? ? ? ? ? ? ? 2.038 ? ? metalc32 metalc ? ? B DC 8 N3 ? ? ? 1_555 R AG . AG ? ? B DC 8 B AG 106 1_555 ? ? ? ? ? ? ? 2.230 ? ? metalc33 metalc ? ? B DG 9 N1 ? ? ? 1_555 O AG . AG ? ? B DG 9 B AG 103 1_555 ? ? ? ? ? ? ? 2.291 ? ? metalc34 metalc ? ? B DG 9 O6 ? ? ? 1_555 Q AG . AG ? ? B DG 9 B AG 105 1_555 ? ? ? ? ? ? ? 2.353 ? ? hydrog1 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DC 3 N4 ? ? A DC 1 A DC 3 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DC 3 O2 ? ? A DC 1 B DC 3 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog3 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DC 4 O2 ? ? A DC 1 B DC 4 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog4 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DA 2 N6 ? ? A DC 3 B DA 2 1_555 ? ? ? ? ? ? 'DC-DA MISPAIR' ? ? ? hydrog5 hydrog ? ? A DC 4 N4 ? ? ? 1_555 A DG 9 O6 ? ? A DC 4 A DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog6 hydrog ? ? A DC 4 O2 ? ? ? 1_555 B DC 1 N4 ? ? A DC 4 B DC 1 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog7 hydrog ? ? A DT 5 O2 ? ? ? 1_555 B DA 6 N6 ? ? A DT 5 B DA 6 1_555 ? ? ? ? ? ? 'DT-DA PAIR' ? ? ? hydrog8 hydrog ? ? A DT 5 O2 ? ? ? 1_555 B DI 7 N1 ? ? A DT 5 B DI 7 1_555 ? ? ? ? ? ? 'DT-DI MISPAIR' ? ? ? hydrog9 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 5 O2 ? ? A DA 6 B DT 5 1_555 ? ? ? ? ? ? 'DA-DT PAIR' ? ? ? hydrog10 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B DC 4 O2 ? ? A DG 9 B DC 4 1_555 ? ? ? ? ? ? 'DG-DC PAIR' ? ? ? hydrog11 hydrog ? ? B DC 1 O2 ? ? ? 1_555 B DC 3 N4 ? ? B DC 1 B DC 3 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog12 hydrog ? ? B DC 4 N4 ? ? ? 1_555 B DG 9 O6 ? ? B DC 4 B DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # _atom_sites.entry_id 7XLV _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] 0.041302 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.024111 _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] 0.022075 _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 C H 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 DA 2 2 2 DA DA A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DT 5 5 5 DT DT A . n A 1 6 DA 6 6 6 DA DA A . n A 1 7 DI 7 7 7 DI DI A . n A 1 8 DC 8 8 8 DC DC A . n A 1 9 DG 9 9 9 DG DG A . n A 1 10 DA 10 10 10 DA DA A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DA 2 2 2 DA DA B . n B 1 3 DC 3 3 3 DC DC B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DT 5 5 5 DT DT B . n B 1 6 DA 6 6 6 DA DA B . n B 1 7 DI 7 7 7 DI DI B . n B 1 8 DC 8 8 8 DC DC B . n B 1 9 DG 9 9 9 DG DG B . n B 1 10 DA 10 10 10 DA DA B . 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 C 2 MPD 1 101 101 MPD MPD A . D 3 AG 1 102 101 AG AG A . E 3 AG 1 103 102 AG AG A . F 3 AG 1 104 103 AG AG A . G 3 AG 1 105 104 AG AG A . H 3 AG 1 106 105 AG AG A . I 3 AG 1 107 106 AG AG A . J 3 AG 1 108 107 AG AG A . K 3 AG 1 109 108 AG AG A . L 3 AG 1 110 109 AG AG A . M 3 AG 1 101 110 AG AG B . N 3 AG 1 102 111 AG AG B . O 3 AG 1 103 112 AG AG B . P 3 AG 1 104 113 AG AG B . Q 3 AG 1 105 114 AG AG B . R 3 AG 1 106 115 AG AG B . S 3 AG 1 107 116 AG AG B . T 3 AG 1 108 117 AG AG B . U 3 AG 1 109 118 AG AG B . V 3 AG 1 110 119 AG AG B . W 4 HOH 1 201 67 HOH HOH A . W 4 HOH 2 202 59 HOH HOH A . W 4 HOH 3 203 36 HOH HOH A . W 4 HOH 4 204 4 HOH HOH A . W 4 HOH 5 205 19 HOH HOH A . W 4 HOH 6 206 55 HOH HOH A . W 4 HOH 7 207 28 HOH HOH A . W 4 HOH 8 208 40 HOH HOH A . W 4 HOH 9 209 11 HOH HOH A . W 4 HOH 10 210 27 HOH HOH A . W 4 HOH 11 211 57 HOH HOH A . W 4 HOH 12 212 66 HOH HOH A . W 4 HOH 13 213 6 HOH HOH A . W 4 HOH 14 214 2 HOH HOH A . W 4 HOH 15 215 10 HOH HOH A . W 4 HOH 16 216 13 HOH HOH A . W 4 HOH 17 217 24 HOH HOH A . W 4 HOH 18 218 23 HOH HOH A . W 4 HOH 19 219 33 HOH HOH A . W 4 HOH 20 220 22 HOH HOH A . W 4 HOH 21 221 51 HOH HOH A . W 4 HOH 22 222 58 HOH HOH A . W 4 HOH 23 223 42 HOH HOH A . W 4 HOH 24 224 49 HOH HOH A . W 4 HOH 25 225 60 HOH HOH A . X 4 HOH 1 201 35 HOH HOH B . X 4 HOH 2 202 29 HOH HOH B . X 4 HOH 3 203 48 HOH HOH B . X 4 HOH 4 204 47 HOH HOH B . X 4 HOH 5 205 9 HOH HOH B . X 4 HOH 6 206 54 HOH HOH B . X 4 HOH 7 207 30 HOH HOH B . X 4 HOH 8 208 18 HOH HOH B . X 4 HOH 9 209 39 HOH HOH B . X 4 HOH 10 210 32 HOH HOH B . X 4 HOH 11 211 63 HOH HOH B . X 4 HOH 12 212 17 HOH HOH B . X 4 HOH 13 213 5 HOH HOH B . X 4 HOH 14 214 3 HOH HOH B . X 4 HOH 15 215 61 HOH HOH B . X 4 HOH 16 216 14 HOH HOH B . X 4 HOH 17 217 26 HOH HOH B . X 4 HOH 18 218 65 HOH HOH B . X 4 HOH 19 219 37 HOH HOH B . X 4 HOH 20 220 50 HOH HOH B . X 4 HOH 21 221 16 HOH HOH B . X 4 HOH 22 222 8 HOH HOH B . X 4 HOH 23 223 56 HOH HOH B . X 4 HOH 24 224 20 HOH HOH B . X 4 HOH 25 225 21 HOH HOH B . X 4 HOH 26 226 15 HOH HOH B . X 4 HOH 27 227 25 HOH HOH B . X 4 HOH 28 228 12 HOH HOH B . X 4 HOH 29 229 64 HOH HOH B . X 4 HOH 30 230 38 HOH HOH B . X 4 HOH 31 231 62 HOH HOH B . X 4 HOH 32 232 34 HOH HOH B . # _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 _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 # 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)' 3460 ? 1 MORE -114 ? 1 'SSA (A^2)' 3000 ? # _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 O2 ? A DC 1 ? A DC 1 ? 1_555 AG ? D AG . ? A AG 102 ? 1_555 N3 ? A DC 3 ? A DC 3 ? 1_555 92.2 ? 2 O2 ? A DC 1 ? A DC 1 ? 1_555 AG ? D AG . ? A AG 102 ? 1_555 N1 ? B DA 2 ? B DA 2 ? 1_555 84.3 ? 3 N3 ? A DC 3 ? A DC 3 ? 1_555 AG ? D AG . ? A AG 102 ? 1_555 N1 ? B DA 2 ? B DA 2 ? 1_555 112.7 ? 4 N3 ? A DC 1 ? A DC 1 ? 1_555 AG ? H AG . ? A AG 106 ? 1_555 O2 ? B DC 3 ? B DC 3 ? 1_555 82.1 ? 5 N3 ? A DC 1 ? A DC 1 ? 1_555 AG ? H AG . ? A AG 106 ? 1_555 O2 ? B DC 4 ? B DC 4 ? 1_555 99.3 ? 6 O2 ? B DC 3 ? B DC 3 ? 1_555 AG ? H AG . ? A AG 106 ? 1_555 O2 ? B DC 4 ? B DC 4 ? 1_555 79.4 ? 7 N3 ? A DC 4 ? A DC 4 ? 1_555 AG ? E AG . ? A AG 103 ? 1_555 O6 ? A DG 9 ? A DG 9 ? 1_555 91.1 ? 8 O2 ? A DC 4 ? A DC 4 ? 1_555 AG ? N AG . ? B AG 102 ? 1_555 N3 ? B DC 1 ? B DC 1 ? 1_555 100.3 ? 9 O2 ? A DC 4 ? A DC 4 ? 1_555 AG ? O AG . ? B AG 103 ? 1_555 N1 ? B DG 9 ? B DG 9 ? 1_555 83.3 ? 10 OP1 ? A DA 6 ? A DA 6 ? 1_555 AG ? G AG . ? A AG 105 ? 1_555 N7 ? A DI 7 ? A DI 7 ? 1_555 92.9 ? 11 N7 ? A DA 6 ? A DA 6 ? 1_555 AG ? K AG . ? A AG 109 ? 1_555 O6 ? A DI 7 ? A DI 7 ? 1_555 92.9 ? 12 N7 ? A DA 6 ? A DA 6 ? 1_555 AG ? K AG . ? A AG 109 ? 1_555 OP2 ? B DA 6 ? B DA 6 ? 1_555 94.8 ? 13 O6 ? A DI 7 ? A DI 7 ? 1_555 AG ? K AG . ? A AG 109 ? 1_555 OP2 ? B DA 6 ? B DA 6 ? 1_555 82.7 ? 14 OP2 ? A DA 6 ? A DA 6 ? 1_555 AG ? P AG . ? B AG 104 ? 1_555 N7 ? B DA 6 ? B DA 6 ? 1_555 90.3 ? 15 OP2 ? A DA 6 ? A DA 6 ? 1_555 AG ? P AG . ? B AG 104 ? 1_555 O6 ? B DI 7 ? B DI 7 ? 1_555 82.9 ? 16 N7 ? B DA 6 ? B DA 6 ? 1_555 AG ? P AG . ? B AG 104 ? 1_555 O6 ? B DI 7 ? B DI 7 ? 1_555 100.5 ? 17 O6 ? A DI 7 ? A DI 7 ? 1_555 AG ? J AG . ? A AG 108 ? 1_555 O2 ? A DC 8 ? A DC 8 ? 1_555 76.4 ? 18 N1 ? A DG 9 ? A DG 9 ? 1_555 AG ? I AG . ? A AG 107 ? 1_555 O2 ? B DC 4 ? B DC 4 ? 1_555 84.8 ? 19 O2 ? B DC 1 ? B DC 1 ? 1_555 AG ? M AG . ? B AG 101 ? 1_555 N3 ? B DC 3 ? B DC 3 ? 1_555 95.3 ? 20 N3 ? B DC 4 ? B DC 4 ? 1_555 AG ? Q AG . ? B AG 105 ? 1_555 O6 ? B DG 9 ? B DG 9 ? 1_555 89.4 ? 21 OP1 ? B DA 6 ? B DA 6 ? 1_555 AG ? S AG . ? B AG 107 ? 1_555 N7 ? B DI 7 ? B DI 7 ? 1_555 88.9 ? # 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 2022-07-13 2 'Structure model' 1 1 2022-10-05 3 'Structure model' 1 2 2023-11-29 # _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' 'Data collection' 3 3 'Structure model' 'Refinement description' # 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' chem_comp_atom 4 3 'Structure model' chem_comp_bond 5 3 'Structure model' pdbx_initial_refinement_model # 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.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_volume' 4 2 'Structure model' '_citation.page_first' 5 2 'Structure model' '_citation.page_last' 6 2 'Structure model' '_citation.pdbx_database_id_DOI' 7 2 'Structure model' '_citation.pdbx_database_id_PubMed' 8 2 '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 extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.27 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 5 # _pdbx_entry_details.entry_id 7XLV _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_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 "C2'" A DI 7 ? ? "C1'" A DI 7 ? ? 1.353 1.524 -0.171 0.020 N 2 1 "O4'" A DI 7 ? ? "C1'" A DI 7 ? ? 1.567 1.410 0.157 0.020 N 3 1 C5 A DI 7 ? ? C6 A DI 7 ? ? 1.528 1.390 0.138 0.020 N 4 1 "C2'" B DI 7 ? ? "C1'" B DI 7 ? ? 1.361 1.524 -0.163 0.020 N 5 1 "O4'" B DI 7 ? ? "C1'" B DI 7 ? ? 1.560 1.410 0.150 0.020 N 6 1 C5 B DI 7 ? ? C6 B DI 7 ? ? 1.532 1.390 0.142 0.020 N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 "O4'" _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 DC _pdbx_validate_rmsd_angle.auth_seq_id_1 4 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 "C1'" _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 DC _pdbx_validate_rmsd_angle.auth_seq_id_2 4 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 N1 _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 DC _pdbx_validate_rmsd_angle.auth_seq_id_3 4 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 111.21 _pdbx_validate_rmsd_angle.angle_target_value 108.30 _pdbx_validate_rmsd_angle.angle_deviation 2.91 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.30 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal AG AG AG N N 1 DA OP3 O N N 2 DA P P N N 3 DA OP1 O N N 4 DA OP2 O N N 5 DA "O5'" O N N 6 DA "C5'" C N N 7 DA "C4'" C N R 8 DA "O4'" O N N 9 DA "C3'" C N S 10 DA "O3'" O N N 11 DA "C2'" C N N 12 DA "C1'" C N R 13 DA N9 N Y N 14 DA C8 C Y N 15 DA N7 N Y N 16 DA C5 C Y N 17 DA C6 C Y N 18 DA N6 N N N 19 DA N1 N Y N 20 DA C2 C Y N 21 DA N3 N Y N 22 DA C4 C Y N 23 DA HOP3 H N N 24 DA HOP2 H N N 25 DA "H5'" H N N 26 DA "H5''" H N N 27 DA "H4'" H N N 28 DA "H3'" H N N 29 DA "HO3'" H N N 30 DA "H2'" H N N 31 DA "H2''" H N N 32 DA "H1'" H N N 33 DA H8 H N N 34 DA H61 H N N 35 DA H62 H N N 36 DA H2 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DG OP3 O N N 72 DG P P N N 73 DG OP1 O N N 74 DG OP2 O N N 75 DG "O5'" O N N 76 DG "C5'" C N N 77 DG "C4'" C N R 78 DG "O4'" O N N 79 DG "C3'" C N S 80 DG "O3'" O N N 81 DG "C2'" C N N 82 DG "C1'" C N R 83 DG N9 N Y N 84 DG C8 C Y N 85 DG N7 N Y N 86 DG C5 C Y N 87 DG C6 C N N 88 DG O6 O N N 89 DG N1 N N N 90 DG C2 C N N 91 DG N2 N N N 92 DG N3 N N N 93 DG C4 C Y N 94 DG HOP3 H N N 95 DG HOP2 H N N 96 DG "H5'" H N N 97 DG "H5''" H N N 98 DG "H4'" H N N 99 DG "H3'" H N N 100 DG "HO3'" H N N 101 DG "H2'" H N N 102 DG "H2''" H N N 103 DG "H1'" H N N 104 DG H8 H N N 105 DG H1 H N N 106 DG H21 H N N 107 DG H22 H N N 108 DI OP3 O N N 109 DI P P N N 110 DI OP1 O N N 111 DI OP2 O N N 112 DI "O5'" O N N 113 DI "C5'" C N N 114 DI "C4'" C N R 115 DI "O4'" O N N 116 DI "C3'" C N S 117 DI "O3'" O N N 118 DI "C2'" C N N 119 DI "C1'" C N R 120 DI N9 N Y N 121 DI C8 C Y N 122 DI N7 N Y N 123 DI C5 C Y N 124 DI C6 C N N 125 DI O6 O N N 126 DI N1 N N N 127 DI C2 C N N 128 DI N3 N N N 129 DI C4 C Y N 130 DI HOP3 H N N 131 DI HOP2 H N N 132 DI "H5'" H N N 133 DI "H5''" H N N 134 DI "H4'" H N N 135 DI "H3'" H N N 136 DI "HO3'" H N N 137 DI "H2'" H N N 138 DI "H2''" H N N 139 DI "H1'" H N N 140 DI H8 H N N 141 DI H1 H N N 142 DI H2 H N N 143 DT OP3 O N N 144 DT P P N N 145 DT OP1 O N N 146 DT OP2 O N N 147 DT "O5'" O N N 148 DT "C5'" C N N 149 DT "C4'" C N R 150 DT "O4'" O N N 151 DT "C3'" C N S 152 DT "O3'" O N N 153 DT "C2'" C N N 154 DT "C1'" C N R 155 DT N1 N N N 156 DT C2 C N N 157 DT O2 O N N 158 DT N3 N N N 159 DT C4 C N N 160 DT O4 O N N 161 DT C5 C N N 162 DT C7 C N N 163 DT C6 C N N 164 DT HOP3 H N N 165 DT HOP2 H N N 166 DT "H5'" H N N 167 DT "H5''" H N N 168 DT "H4'" H N N 169 DT "H3'" H N N 170 DT "HO3'" H N N 171 DT "H2'" H N N 172 DT "H2''" H N N 173 DT "H1'" H N N 174 DT H3 H N N 175 DT H71 H N N 176 DT H72 H N N 177 DT H73 H N N 178 DT H6 H N N 179 HOH O O N N 180 HOH H1 H N N 181 HOH H2 H N N 182 MPD C1 C N N 183 MPD C2 C N N 184 MPD O2 O N N 185 MPD CM C N N 186 MPD C3 C N N 187 MPD C4 C N S 188 MPD O4 O N N 189 MPD C5 C N N 190 MPD H11 H N N 191 MPD H12 H N N 192 MPD H13 H N N 193 MPD HO2 H N N 194 MPD HM1 H N N 195 MPD HM2 H N N 196 MPD HM3 H N N 197 MPD H31 H N N 198 MPD H32 H N N 199 MPD H4 H N N 200 MPD HO4 H N N 201 MPD H51 H N N 202 MPD H52 H N N 203 MPD H53 H N N 204 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DI OP3 P sing N N 113 DI OP3 HOP3 sing N N 114 DI P OP1 doub N N 115 DI P OP2 sing N N 116 DI P "O5'" sing N N 117 DI OP2 HOP2 sing N N 118 DI "O5'" "C5'" sing N N 119 DI "C5'" "C4'" sing N N 120 DI "C5'" "H5'" sing N N 121 DI "C5'" "H5''" sing N N 122 DI "C4'" "O4'" sing N N 123 DI "C4'" "C3'" sing N N 124 DI "C4'" "H4'" sing N N 125 DI "O4'" "C1'" sing N N 126 DI "C3'" "O3'" sing N N 127 DI "C3'" "C2'" sing N N 128 DI "C3'" "H3'" sing N N 129 DI "O3'" "HO3'" sing N N 130 DI "C2'" "C1'" sing N N 131 DI "C2'" "H2'" sing N N 132 DI "C2'" "H2''" sing N N 133 DI "C1'" N9 sing N N 134 DI "C1'" "H1'" sing N N 135 DI N9 C8 sing Y N 136 DI N9 C4 sing Y N 137 DI C8 N7 doub Y N 138 DI C8 H8 sing N N 139 DI N7 C5 sing Y N 140 DI C5 C6 sing N N 141 DI C5 C4 doub Y N 142 DI C6 O6 doub N N 143 DI C6 N1 sing N N 144 DI N1 C2 sing N N 145 DI N1 H1 sing N N 146 DI C2 N3 doub N N 147 DI C2 H2 sing N N 148 DI N3 C4 sing N N 149 DT OP3 P sing N N 150 DT OP3 HOP3 sing N N 151 DT P OP1 doub N N 152 DT P OP2 sing N N 153 DT P "O5'" sing N N 154 DT OP2 HOP2 sing N N 155 DT "O5'" "C5'" sing N N 156 DT "C5'" "C4'" sing N N 157 DT "C5'" "H5'" sing N N 158 DT "C5'" "H5''" sing N N 159 DT "C4'" "O4'" sing N N 160 DT "C4'" "C3'" sing N N 161 DT "C4'" "H4'" sing N N 162 DT "O4'" "C1'" sing N N 163 DT "C3'" "O3'" sing N N 164 DT "C3'" "C2'" sing N N 165 DT "C3'" "H3'" sing N N 166 DT "O3'" "HO3'" sing N N 167 DT "C2'" "C1'" sing N N 168 DT "C2'" "H2'" sing N N 169 DT "C2'" "H2''" sing N N 170 DT "C1'" N1 sing N N 171 DT "C1'" "H1'" sing N N 172 DT N1 C2 sing N N 173 DT N1 C6 sing N N 174 DT C2 O2 doub N N 175 DT C2 N3 sing N N 176 DT N3 C4 sing N N 177 DT N3 H3 sing N N 178 DT C4 O4 doub N N 179 DT C4 C5 sing N N 180 DT C5 C7 sing N N 181 DT C5 C6 doub N N 182 DT C7 H71 sing N N 183 DT C7 H72 sing N N 184 DT C7 H73 sing N N 185 DT C6 H6 sing N N 186 HOH O H1 sing N N 187 HOH O H2 sing N N 188 MPD C1 C2 sing N N 189 MPD C1 H11 sing N N 190 MPD C1 H12 sing N N 191 MPD C1 H13 sing N N 192 MPD C2 O2 sing N N 193 MPD C2 CM sing N N 194 MPD C2 C3 sing N N 195 MPD O2 HO2 sing N N 196 MPD CM HM1 sing N N 197 MPD CM HM2 sing N N 198 MPD CM HM3 sing N N 199 MPD C3 C4 sing N N 200 MPD C3 H31 sing N N 201 MPD C3 H32 sing N N 202 MPD C4 O4 sing N N 203 MPD C4 C5 sing N N 204 MPD C4 H4 sing N N 205 MPD O4 HO4 sing N N 206 MPD C5 H51 sing N N 207 MPD C5 H52 sing N N 208 MPD C5 H53 sing N N 209 # _ndb_struct_conf_na.entry_id 7XLV _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 DC 4 1_555 -1.333 3.276 -0.165 -20.336 -34.168 86.966 1 A_DC1:DC4_B A 1 ? B 4 ? ? ? 1 B DC 1 1_555 B DC 3 1_555 1.512 -3.092 0.719 -36.427 19.586 -86.171 2 B_DC1:DC3_B B 1 ? B 3 ? ? ? 1 A DC 3 1_555 B DA 2 1_555 1.243 -1.879 0.630 22.603 28.658 -124.369 3 A_DC3:DA2_B A 3 ? B 2 ? ? ? 1 A DT 5 1_555 B DA 6 1_555 3.358 -3.932 0.649 -27.785 -10.989 -72.587 4 A_DT5:DA6_B A 5 ? B 6 ? ? ? 1 A DA 6 1_555 B DT 5 1_555 -3.016 3.611 0.664 23.459 25.585 73.507 5 A_DA6:DT5_B A 6 ? B 5 ? ? ? # 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 DC 4 1_555 B DC 1 1_555 B DC 3 1_555 1.529 -2.587 -0.771 -31.889 40.312 -101.330 1.617 0.964 0.270 -25.012 -19.785 -110.339 1 AB_DC1DC1:DC3DC4_BB A 1 ? B 4 ? B 1 ? B 3 ? 1 B DC 1 1_555 B DC 3 1_555 A DC 3 1_555 B DA 2 1_555 -0.912 -1.730 -3.183 1.670 4.753 -71.284 1.636 -0.835 -3.059 -4.073 1.431 -71.439 2 BA_DC1DC3:DA2DC3_BB B 1 ? B 3 ? A 3 ? B 2 ? # _pdbx_audit_support.funding_organization 'Danish Council for Independent Research' _pdbx_audit_support.country Denmark _pdbx_audit_support.grant_number 0136-00024B _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 '(4S)-2-METHYL-2,4-PENTANEDIOL' MPD 3 'SILVER ION' AG 4 water HOH # _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name PDB _pdbx_initial_refinement_model.accession_code 6JR4 _pdbx_initial_refinement_model.details ? # _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 ? #