data_9KHW # _entry.id 9KHW # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.402 _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 9KHW pdb_00009khw 10.2210/pdb9khw/pdb WWPDB D_1300053210 ? ? # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2025-04-02 _pdbx_audit_revision_history.part_number ? # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 9KHW _pdbx_database_status.recvd_initial_deposition_date 2024-11-11 _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_ _pdbx_contact_author.id _pdbx_contact_author.email _pdbx_contact_author.name_first _pdbx_contact_author.name_last _pdbx_contact_author.name_mi _pdbx_contact_author.role _pdbx_contact_author.identifier_ORCID 3 j.kondo@sophia.ac.jp Kondo Jiro ? 'principal investigator/group leader' 0000-0002-5682-3685 4 tom@chem.ku.dk Tom Vosch ? 'principal investigator/group leader' 0000-0001-5435-2181 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Kanazawa, H.' 1 ? 'Kondo, J.' 2 ? 'Romolini, G.' 3 ? 'Cerretani, C.' 4 ? 'Lanza, A.' 5 ? 'Huang, Z.' 6 ? 'Vosch, T.' 7 ? # _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 DE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Small Struct' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2688-4062 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Shining Bright at 960 nm: A 28-Silver-Atom Nanorod Stabilized by DNA' _citation.year 2025 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/sstr.202500022 _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Romolini, G.' 1 ? primary 'Kanazawa, H.' 2 ? primary 'Mollerup, C.' 3 ? primary 'Lisberg, M.' 4 ? primary 'Lind, S.' 5 ? primary 'Huang, Z.' 6 ? primary 'Cerretani, C.' 7 ? primary 'Kondo, J.' 8 ? primary 'Vosch, T.' 9 ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*CP*CP*GP*CP*GP*CP*GP*CP*GP*CP*CP*GP*CP*GP*AP*A)-3') ; 4870.146 2 ? ? ? ? 2 non-polymer syn 'SILVER ION' 107.868 28 ? ? ? ? 3 non-polymer syn 'CHLORIDE ION' 35.453 2 ? ? ? ? 4 water nat water 18.015 39 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DG)(DC)(DC)(DG)(DC)(DG)(DA)(DA)' _entity_poly.pdbx_seq_one_letter_code_can CCGCGCGCGCCGCGAA _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SILVER ION' AG 3 'CHLORIDE ION' CL 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DC n 1 3 DG n 1 4 DC n 1 5 DG n 1 6 DC n 1 7 DG n 1 8 DC n 1 9 DG n 1 10 DC n 1 11 DC n 1 12 DG n 1 13 DC n 1 14 DG n 1 15 DA n 1 16 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 16 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight AG non-polymer . 'SILVER ION' ? 'Ag 1' 107.868 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 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 HOH non-polymer . WATER ? 'H2 O' 18.015 # 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 DC 2 2 2 DC DC A . n A 1 3 DG 3 3 3 DG DG A . n A 1 4 DC 4 4 4 DC DC A . n A 1 5 DG 5 5 5 DG DG A . n A 1 6 DC 6 6 6 DC DC A . n A 1 7 DG 7 7 7 DG DG 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 DC 10 10 10 DC DC A . n A 1 11 DC 11 11 11 DC DC A . n A 1 12 DG 12 12 12 DG DG A . n A 1 13 DC 13 13 13 DC DC A . n A 1 14 DG 14 14 14 DG DG A . n A 1 15 DA 15 15 15 DA DA A . n A 1 16 DA 16 16 16 DA DA A . n B 1 1 DC 1 1 1 DC DC B . n B 1 2 DC 2 2 2 DC DC B . n B 1 3 DG 3 3 3 DG DG B . n B 1 4 DC 4 4 4 DC DC B . n B 1 5 DG 5 5 5 DG DG B . n B 1 6 DC 6 6 6 DC DC B . n B 1 7 DG 7 7 7 DG DG 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 DC 10 10 10 DC DC B . n B 1 11 DC 11 11 11 DC DC B . n B 1 12 DG 12 12 12 DG DG B . n B 1 13 DC 13 13 13 DC DC B . n B 1 14 DG 14 14 14 DG DG B . n B 1 15 DA 15 15 15 DA DA B . n B 1 16 DA 16 16 16 DA DA B . n # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 CL ? ? CL ? ? 'SUBJECT OF INVESTIGATION' ? 2 AG ? ? AG ? ? 'SUBJECT OF INVESTIGATION' ? # 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 AG 1 101 1 AG AG A . D 2 AG 1 102 2 AG AG A . E 2 AG 1 103 3 AG AG A . F 2 AG 1 104 4 AG AG A . G 2 AG 1 105 5 AG AG A . H 2 AG 1 106 6 AG AG A . I 2 AG 1 107 7 AG AG A . J 2 AG 1 108 8 AG AG A . K 2 AG 1 109 9 AG AG A . L 2 AG 1 110 10 AG AG A . M 2 AG 1 111 11 AG AG A . N 2 AG 1 112 12 AG AG A . O 2 AG 1 113 13 AG AG A . P 2 AG 1 114 14 AG AG A . Q 3 CL 1 115 1 CL CL A . R 2 AG 1 101 15 AG AG B . S 2 AG 1 102 16 AG AG B . T 2 AG 1 103 17 AG AG B . U 2 AG 1 104 18 AG AG B . V 2 AG 1 105 19 AG AG B . W 2 AG 1 106 20 AG AG B . X 2 AG 1 107 21 AG AG B . Y 2 AG 1 108 22 AG AG B . Z 2 AG 1 109 23 AG AG B . AA 2 AG 1 110 24 AG AG B . BA 2 AG 1 111 25 AG AG B . CA 2 AG 1 112 26 AG AG B . DA 2 AG 1 113 27 AG AG B . EA 2 AG 1 114 28 AG AG B . FA 3 CL 1 115 2 CL CL B . GA 4 HOH 1 201 1 HOH HOH A . GA 4 HOH 2 202 25 HOH HOH A . GA 4 HOH 3 203 22 HOH HOH A . GA 4 HOH 4 204 21 HOH HOH A . GA 4 HOH 5 205 11 HOH HOH A . GA 4 HOH 6 206 8 HOH HOH A . GA 4 HOH 7 207 3 HOH HOH A . GA 4 HOH 8 208 6 HOH HOH A . GA 4 HOH 9 209 12 HOH HOH A . GA 4 HOH 10 210 19 HOH HOH A . GA 4 HOH 11 211 33 HOH HOH A . GA 4 HOH 12 212 4 HOH HOH A . GA 4 HOH 13 213 32 HOH HOH A . GA 4 HOH 14 214 15 HOH HOH A . GA 4 HOH 15 215 16 HOH HOH A . GA 4 HOH 16 216 31 HOH HOH A . GA 4 HOH 17 217 36 HOH HOH A . HA 4 HOH 1 201 14 HOH HOH B . HA 4 HOH 2 202 34 HOH HOH B . HA 4 HOH 3 203 17 HOH HOH B . HA 4 HOH 4 204 24 HOH HOH B . HA 4 HOH 5 205 10 HOH HOH B . HA 4 HOH 6 206 18 HOH HOH B . HA 4 HOH 7 207 7 HOH HOH B . HA 4 HOH 8 208 2 HOH HOH B . HA 4 HOH 9 209 26 HOH HOH B . HA 4 HOH 10 210 9 HOH HOH B . HA 4 HOH 11 211 13 HOH HOH B . HA 4 HOH 12 212 28 HOH HOH B . HA 4 HOH 13 213 5 HOH HOH B . HA 4 HOH 14 214 39 HOH HOH B . HA 4 HOH 15 215 29 HOH HOH B . HA 4 HOH 16 216 20 HOH HOH B . HA 4 HOH 17 217 27 HOH HOH B . HA 4 HOH 18 218 23 HOH HOH B . HA 4 HOH 19 219 30 HOH HOH B . HA 4 HOH 20 220 35 HOH HOH B . HA 4 HOH 21 221 38 HOH HOH B . HA 4 HOH 22 222 37 HOH HOH B . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(1.20.1_4487: ???)' 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? XSCALE ? ? ? . 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? Sir2014 ? ? ? Sir2019 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? AutoSol ? ? ? . 4 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? XDS ? ? ? . 5 # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 103.67 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 9KHW _cell.details ? _cell.formula_units_Z ? _cell.length_a 27.215 _cell.length_a_esd ? _cell.length_b 53.171 _cell.length_b_esd ? _cell.length_c 27.215 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 4 _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 9KHW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 9KHW _exptl.crystals_number 2 _exptl.details ? _exptl.method 'X-RAY DIFFRACTION' _exptl.method_details ? # loop_ _exptl_crystal.colour _exptl_crystal.density_diffrn _exptl_crystal.density_Matthews _exptl_crystal.density_method _exptl_crystal.density_percent_sol _exptl_crystal.description _exptl_crystal.F_000 _exptl_crystal.id _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 ? ? 1.96 ? 37.38 ? ? 1 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 2 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _exptl_crystal_grow.apparatus _exptl_crystal_grow.atmosphere _exptl_crystal_grow.crystal_id _exptl_crystal_grow.details _exptl_crystal_grow.method _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_details _exptl_crystal_grow.temp_esd _exptl_crystal_grow.time _exptl_crystal_grow.pdbx_details _exptl_crystal_grow.pdbx_pH_range _exptl_crystal_grow.temp ? ? 1 ? 'VAPOR DIFFUSION, SITTING DROP' ? 7.0 ? ? ? ? ? ? ? '50 mM MOPS, 10 mM spermine, 10 mM KNO3, 10% MPD' ? 293 ? ? 2 ? 'VAPOR DIFFUSION, HANGING DROP' ? 7.0 ? ? ? ? ? ? ? ;50 mM 3-(N-morpholino)propanesulfonic acid, 10 mM spermine, 10 mM Ca(NO3), 10% 2-methyl-2,4-pentanediol against a reservoir solution of 40% 2-methyl-2,4-pentanediol. ; ? 293 # loop_ _diffrn.ambient_environment _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.ambient_temp_esd _diffrn.crystal_id _diffrn.crystal_support _diffrn.crystal_treatment _diffrn.details _diffrn.id _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 ? 100 ? ? 1 ? ? ? 1 ? ? ? ? ? ? Y ? 100 ? ? 2 ? ? ? 2 ? ? ? ? ? ? Y # loop_ _diffrn_detector.details _diffrn_detector.detector _diffrn_detector.diffrn_id _diffrn_detector.type _diffrn_detector.area_resol_mean _diffrn_detector.dtime _diffrn_detector.pdbx_frames_total _diffrn_detector.pdbx_collection_time_total _diffrn_detector.pdbx_collection_date _diffrn_detector.pdbx_frequency _diffrn_detector.id _diffrn_detector.number_of_axes ? PIXEL 1 'DECTRIS PILATUS 6M' ? ? ? ? 2024-10-12 ? ? ? ? PIXEL 2 'DECTRIS EIGER2 S 16M' ? ? ? ? 2024-10-20 ? ? ? # loop_ _diffrn_radiation.collimation _diffrn_radiation.diffrn_id _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 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.pdbx_wavelength_list _diffrn_radiation.pdbx_wavelength _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_analyzer _diffrn_radiation.pdbx_scattering_type ? 1 ? ? ? ? ? ? ? ? 1 M ? ? 'SINGLE WAVELENGTH' ? x-ray ? 2 ? ? ? ? ? ? ? ? 2 M ? ? 'SINGLE WAVELENGTH' ? x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.9 1.0 2 0.6199 1.0 # loop_ _diffrn_source.current _diffrn_source.details _diffrn_source.diffrn_id _diffrn_source.power _diffrn_source.size _diffrn_source.source _diffrn_source.target _diffrn_source.type _diffrn_source.voltage _diffrn_source.take-off_angle _diffrn_source.pdbx_wavelength_list _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_synchrotron_site ? ? 1 ? ? SYNCHROTRON ? 'PHOTON FACTORY BEAMLINE BL-5A' ? ? 1.9 ? BL-5A 'Photon Factory' ? ? 2 ? ? SYNCHROTRON ? 'MAX IV BEAMLINE BioMAX' ? ? 0.6199 ? BioMAX 'MAX IV' # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 9KHW _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.3 _reflns.d_resolution_low 26.4 _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 35689 _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 97.1 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 3.6 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 7.25 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.pdbx_d_res_opt_method ? _reflns.phase_calculation_details ? _reflns.pdbx_Rrim_I_all 0.13 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 2 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half 0.993 _reflns.pdbx_CC_star ? _reflns.pdbx_R_split ? _reflns.pdbx_Rmerge_I_obs 0.111 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_CC_split_method ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] ? _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] ? _reflns.pdbx_aniso_diffraction_limit_1 ? _reflns.pdbx_aniso_diffraction_limit_2 ? _reflns.pdbx_aniso_diffraction_limit_3 ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_1_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_2_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[1] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[2] ? _reflns.pdbx_aniso_B_tensor_eigenvector_3_ortho[3] ? _reflns.pdbx_aniso_B_tensor_eigenvalue_1 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_2 ? _reflns.pdbx_aniso_B_tensor_eigenvalue_3 ? _reflns.pdbx_orthogonalization_convention ? _reflns.pdbx_percent_possible_ellipsoidal ? _reflns.pdbx_percent_possible_spherical ? _reflns.pdbx_percent_possible_ellipsoidal_anomalous ? _reflns.pdbx_percent_possible_spherical_anomalous ? _reflns.pdbx_redundancy_anomalous ? _reflns.pdbx_CC_half_anomalous ? _reflns.pdbx_absDiff_over_sigma_anomalous ? _reflns.pdbx_percent_possible_anomalous ? _reflns.pdbx_observed_signal_threshold ? _reflns.pdbx_signal_type ? _reflns.pdbx_signal_details ? _reflns.pdbx_signal_software_id ? # 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_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_CC_star _reflns_shell.pdbx_R_split _reflns_shell.percent_possible_all _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_percent_possible_ellipsoidal _reflns_shell.pdbx_percent_possible_spherical _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous _reflns_shell.pdbx_percent_possible_spherical_anomalous _reflns_shell.pdbx_redundancy_anomalous _reflns_shell.pdbx_CC_half_anomalous _reflns_shell.pdbx_absDiff_over_sigma_anomalous _reflns_shell.pdbx_percent_possible_anomalous 1.30 1.33 ? ? ? ? ? ? 2549 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.376 ? ? 1 2 0.899 ? ? ? ? 0.319 ? ? ? ? ? ? ? ? ? 1.33 1.37 ? ? ? ? ? ? 2543 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.339 ? ? 2 2 0.918 ? ? ? ? 0.288 ? ? ? ? ? ? ? ? ? 1.37 1.41 ? ? ? ? ? ? 2478 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.314 ? ? 3 2 0.939 ? ? ? ? 0.266 ? ? ? ? ? ? ? ? ? 1.41 1.45 ? ? ? ? ? ? 2443 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.315 ? ? 4 2 0.933 ? ? ? ? 0.267 ? ? ? ? ? ? ? ? ? 1.45 1.5 ? ? ? ? ? ? 2414 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.291 ? ? 5 2 0.938 ? ? ? ? 0.247 ? ? ? ? ? ? ? ? ? 1.50 1.55 ? ? ? ? ? ? 2202 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.295 ? ? 6 2 0.931 ? ? ? ? 0.249 ? ? ? ? ? ? ? ? ? 1.55 1.61 ? ? ? ? ? ? 2257 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.275 ? ? 7 2 0.951 ? ? ? ? 0.235 ? ? ? ? ? ? ? ? ? 1.61 1.67 ? ? ? ? ? ? 2089 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.238 ? ? 8 2 0.96 ? ? ? ? 0.203 ? ? ? ? ? ? ? ? ? 1.67 1.75 ? ? ? ? ? ? 2071 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.216 ? ? 9 2 0.962 ? ? ? ? 0.184 ? ? ? ? ? ? ? ? ? 1.75 1.83 ? ? ? ? ? ? 1967 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.181 ? ? 10 2 0.973 ? ? ? ? 0.154 ? ? ? ? ? ? ? ? ? 1.83 1.93 ? ? ? ? ? ? 1919 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.156 ? ? 11 2 0.982 ? ? ? ? 0.133 ? ? ? ? ? ? ? ? ? 1.93 2.05 ? ? ? ? ? ? 1737 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.12 ? ? 12 2 0.987 ? ? ? ? 0.102 ? ? ? ? ? ? ? ? ? 2.05 2.19 ? ? ? ? ? ? 1646 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.104 ? ? 13 2 0.989 ? ? ? ? 0.089 ? ? ? ? ? ? ? ? ? 2.19 2.37 ? ? ? ? ? ? 1539 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.087 ? ? 14 2 0.992 ? ? ? ? 0.074 ? ? ? ? ? ? ? ? ? 2.37 2.59 ? ? ? ? ? ? 1371 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.08 ? ? 15 2 0.996 ? ? ? ? 0.068 ? ? ? ? ? ? ? ? ? 2.59 2.9 ? ? ? ? ? ? 1268 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.089 ? ? 16 2 0.991 ? ? ? ? 0.076 ? ? ? ? ? ? ? ? ? 2.90 3.35 ? ? ? ? ? ? 1143 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.079 ? ? 17 2 0.995 ? ? ? ? 0.068 ? ? ? ? ? ? ? ? ? 3.35 4.1 ? ? ? ? ? ? 939 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.077 ? ? 18 2 0.995 ? ? ? ? 0.067 ? ? ? ? ? ? ? ? ? 4.10 5.8 ? ? ? ? ? ? 742 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.074 ? ? 19 2 0.994 ? ? ? ? 0.063 ? ? ? ? ? ? ? ? ? 5.80 26.4 ? ? ? ? ? ? 372 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 0.065 ? ? 20 2 0.995 ? ? ? ? 0.056 ? ? ? ? ? ? ? ? ? 2.0 26.6 ? ? ? ? ? ? 9236 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? 21 1 0.994 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max ? _refine.B_iso_mean ? _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 9KHW _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 1.30 _refine.ls_d_res_low 16.82 _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 35654 _refine.ls_number_reflns_R_free 3521 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 97.16 _refine.ls_percent_reflns_R_free 9.88 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1632 _refine.ls_R_factor_R_free 0.1642 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1631 _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 1.98 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _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 1.10 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.90 _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 19.95 _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 0.10 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.details ? _refine_hist.d_res_high 1.30 _refine_hist.d_res_low 16.82 _refine_hist.number_atoms_solvent 39 _refine_hist.number_atoms_total 715 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 646 _refine_hist.pdbx_number_atoms_ligand 30 _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' ? 0.009 ? 724 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.210 ? 1112 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 28.714 ? 312 ? f_dihedral_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.097 ? 126 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.018 ? 32 ? f_plane_restr ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_R_complete _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error _refine_ls_shell.pdbx_fsc_work _refine_ls_shell.pdbx_fsc_free _refine_ls_shell.R_factor_R_free 'X-RAY DIFFRACTION' 1.30 1.31 . . 132 1189 96.00 . . . . 0.2335 . . . . . . . . . . . 0.2676 'X-RAY DIFFRACTION' 1.31 1.33 . . 138 1257 96.00 . . . . 0.2342 . . . . . . . . . . . 0.2502 'X-RAY DIFFRACTION' 1.33 1.35 . . 146 1303 97.00 . . . . 0.2214 . . . . . . . . . . . 0.2243 'X-RAY DIFFRACTION' 1.35 1.37 . . 143 1280 96.00 . . . . 0.2155 . . . . . . . . . . . 0.2757 'X-RAY DIFFRACTION' 1.37 1.40 . . 139 1244 96.00 . . . . 0.2181 . . . . . . . . . . . 0.2001 'X-RAY DIFFRACTION' 1.40 1.42 . . 142 1318 98.00 . . . . 0.2176 . . . . . . . . . . . 0.1800 'X-RAY DIFFRACTION' 1.42 1.45 . . 136 1272 97.00 . . . . 0.2127 . . . . . . . . . . . 0.1995 'X-RAY DIFFRACTION' 1.45 1.47 . . 147 1337 98.00 . . . . 0.2026 . . . . . . . . . . . 0.1992 'X-RAY DIFFRACTION' 1.47 1.50 . . 143 1276 97.00 . . . . 0.2146 . . . . . . . . . . . 0.1946 'X-RAY DIFFRACTION' 1.50 1.54 . . 147 1256 97.00 . . . . 0.2155 . . . . . . . . . . . 0.2174 'X-RAY DIFFRACTION' 1.54 1.57 . . 140 1311 97.00 . . . . 0.1921 . . . . . . . . . . . 0.2367 'X-RAY DIFFRACTION' 1.57 1.61 . . 142 1291 98.00 . . . . 0.2110 . . . . . . . . . . . 0.2775 'X-RAY DIFFRACTION' 1.61 1.66 . . 139 1287 98.00 . . . . 0.1801 . . . . . . . . . . . 0.2026 'X-RAY DIFFRACTION' 1.66 1.70 . . 148 1335 98.00 . . . . 0.1841 . . . . . . . . . . . 0.1607 'X-RAY DIFFRACTION' 1.70 1.76 . . 141 1258 98.00 . . . . 0.1702 . . . . . . . . . . . 0.1409 'X-RAY DIFFRACTION' 1.76 1.82 . . 145 1323 98.00 . . . . 0.1652 . . . . . . . . . . . 0.1497 'X-RAY DIFFRACTION' 1.82 1.89 . . 136 1283 98.00 . . . . 0.1396 . . . . . . . . . . . 0.1351 'X-RAY DIFFRACTION' 1.89 1.98 . . 145 1309 98.00 . . . . 0.1281 . . . . . . . . . . . 0.1499 'X-RAY DIFFRACTION' 1.98 2.08 . . 137 1310 98.00 . . . . 0.1284 . . . . . . . . . . . 0.1304 'X-RAY DIFFRACTION' 2.09 2.21 . . 125 1313 98.00 . . . . 0.1232 . . . . . . . . . . . 0.1258 'X-RAY DIFFRACTION' 2.21 2.39 . . 144 1294 97.00 . . . . 0.1226 . . . . . . . . . . . 0.1093 'X-RAY DIFFRACTION' 2.39 2.62 . . 149 1239 96.00 . . . . 0.1157 . . . . . . . . . . . 0.1062 'X-RAY DIFFRACTION' 2.62 3.00 . . 133 1298 97.00 . . . . 0.1430 . . . . . . . . . . . 0.1635 'X-RAY DIFFRACTION' 3.00 3.78 . . 138 1302 98.00 . . . . 0.1657 . . . . . . . . . . . 0.1747 'X-RAY DIFFRACTION' 3.78 16.82 . . 146 1248 95.00 . . . . 0.1688 . . . . . . . . . . . 0.1749 # _struct.entry_id 9KHW _struct.title 'A DNA-stabilized atomically precise silver nanorod with emission at 960 nm' _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 9KHW _struct_keywords.text 'DNA, silver, Ag28, near infrared emission, fluorescence, DNA-AgNC' _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 2 ? 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 3 ? 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 2 ? CA N N 2 ? DA N N 2 ? EA N N 2 ? FA N N 3 ? GA N N 4 ? HA N N 4 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 9KHW _struct_ref.pdbx_db_accession 9KHW _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 9KHW A 1 ? 16 ? 9KHW 1 ? 16 ? 1 16 2 1 9KHW B 1 ? 16 ? 9KHW 1 ? 16 ? 1 16 # _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 # 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)' 5790 ? 1 MORE -196 ? 1 'SSA (A^2)' 3790 ? # _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,FA,GA,HA # _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 'Electron Dispersive X-ray Spectroscopy' # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A DC 1 O2 ? ? ? 1_555 I AG . AG ? ? A DC 1 A AG 107 1_555 ? ? ? ? ? ? ? 2.306 ? ? metalc2 metalc ? ? A DC 1 N3 ? ? ? 1_555 L AG . AG ? ? A DC 1 A AG 110 1_555 ? ? ? ? ? ? ? 2.372 ? ? metalc3 metalc ? ? A DC 2 N3 ? ? ? 1_555 D AG . AG ? ? A DC 2 A AG 102 1_555 ? ? ? ? ? ? ? 2.284 ? ? metalc4 metalc ? ? A DC 2 O2 ? ? ? 1_555 G AG . AG ? ? A DC 2 A AG 105 1_555 ? ? ? ? ? ? ? 2.632 ? ? metalc5 metalc ? ? A DG 3 N7 ? ? ? 1_555 C AG . AG ? ? A DG 3 A AG 101 1_555 ? ? ? ? ? ? ? 2.303 ? ? metalc6 metalc ? ? A DC 4 O2 ? ? ? 1_555 F AG . AG ? ? A DC 4 A AG 104 1_555 ? ? ? ? ? ? ? 2.370 ? ? metalc7 metalc ? ? A DC 4 N3 ? ? ? 1_555 G AG . AG ? ? A DC 4 A AG 105 1_555 ? ? ? ? ? ? ? 2.285 ? ? metalc8 metalc ? ? A DG 5 N7 ? ? ? 1_555 J AG . AG ? ? A DG 5 A AG 108 1_555 ? ? ? ? ? ? ? 2.235 ? ? metalc9 metalc ? ? A DG 5 O6 ? ? ? 1_555 L AG . AG ? ? A DG 5 A AG 110 1_555 ? ? ? ? ? ? ? 2.513 ? ? metalc10 metalc ? ? A DC 6 O2 ? ? ? 1_555 M AG . AG ? ? A DC 6 A AG 111 1_555 ? ? ? ? ? ? ? 2.495 ? ? metalc11 metalc ? ? A DC 6 N3 ? ? ? 1_555 N AG . AG ? ? A DC 6 A AG 112 1_555 ? ? ? ? ? ? ? 2.225 ? ? metalc12 metalc ? ? A DG 7 O6 ? ? ? 1_555 O AG . AG ? ? A DG 7 A AG 113 1_555 ? ? ? ? ? ? ? 2.652 ? ? metalc13 metalc ? ? A DG 7 N7 ? ? ? 1_555 P AG . AG ? ? A DG 7 A AG 114 1_555 ? ? ? ? ? ? ? 2.312 ? ? metalc14 metalc ? ? A DG 9 O6 ? ? ? 1_555 K AG . AG ? ? A DG 9 A AG 109 1_555 ? ? ? ? ? ? ? 2.200 ? ? metalc15 metalc ? ? A DG 9 N1 ? ? ? 1_555 M AG . AG ? ? A DG 9 A AG 111 1_555 ? ? ? ? ? ? ? 2.305 ? ? metalc16 metalc ? ? A DC 10 O2 ? ? ? 1_555 F AG . AG ? ? A DC 10 A AG 104 1_555 ? ? ? ? ? ? ? 2.480 ? ? metalc17 metalc ? ? A DC 10 N3 ? ? ? 1_555 H AG . AG ? ? A DC 10 A AG 106 1_555 ? ? ? ? ? ? ? 2.348 ? ? metalc18 metalc ? ? A DC 11 O2 ? ? ? 1_555 E AG . AG ? ? A DC 11 A AG 103 1_555 ? ? ? ? ? ? ? 2.363 ? ? metalc19 metalc ? ? A DC 11 N3 ? ? ? 1_555 F AG . AG ? ? A DC 11 A AG 104 1_555 ? ? ? ? ? ? ? 2.441 ? ? metalc20 metalc ? ? A DG 12 N7 ? ? ? 1_555 C AG . AG ? ? A DG 12 A AG 101 1_555 ? ? ? ? ? ? ? 2.415 ? ? metalc21 metalc ? ? A DC 13 O2 ? ? ? 1_555 D AG . AG ? ? A DC 13 A AG 102 1_555 ? ? ? ? ? ? ? 2.604 ? ? metalc22 metalc ? ? A DC 13 N3 ? ? ? 1_555 E AG . AG ? ? A DC 13 A AG 103 1_555 ? ? ? ? ? ? ? 2.313 ? ? metalc23 metalc ? ? A DG 14 O6 ? ? ? 1_555 H AG . AG ? ? A DG 14 A AG 106 1_555 ? ? ? ? ? ? ? 2.352 ? ? metalc24 metalc ? ? A DG 14 N1 ? ? ? 1_555 I AG . AG ? ? A DG 14 A AG 107 1_555 ? ? ? ? ? ? ? 2.377 ? ? metalc25 metalc ? ? A DA 15 N1 ? ? ? 1_555 K AG . AG ? ? A DA 15 A AG 109 1_555 ? ? ? ? ? ? ? 2.345 ? ? metalc26 metalc ? ? A DA 16 N1 ? ? ? 1_555 O AG . AG ? ? A DA 16 A AG 113 1_555 ? ? ? ? ? ? ? 2.271 ? ? metalc27 metalc ? ? B DC 1 N3 ? ? ? 1_555 W AG . AG ? ? B DC 1 B AG 106 1_555 ? ? ? ? ? ? ? 2.377 ? ? metalc28 metalc ? ? B DC 1 O2 ? ? ? 1_555 Y AG . AG ? ? B DC 1 B AG 108 1_555 ? ? ? ? ? ? ? 2.314 ? ? metalc29 metalc ? ? B DC 2 O2 ? ? ? 1_555 AA AG . AG ? ? B DC 2 B AG 110 1_555 ? ? ? ? ? ? ? 2.642 ? ? metalc30 metalc ? ? B DC 2 N3 ? ? ? 1_555 CA AG . AG ? ? B DC 2 B AG 112 1_555 ? ? ? ? ? ? ? 2.289 ? ? metalc31 metalc ? ? B DG 3 N7 ? ? ? 1_555 EA AG . AG ? ? B DG 3 B AG 114 1_555 ? ? ? ? ? ? ? 2.305 ? ? metalc32 metalc ? ? B DC 4 N3 ? ? ? 1_555 AA AG . AG ? ? B DC 4 B AG 110 1_555 ? ? ? ? ? ? ? 2.233 ? ? metalc33 metalc ? ? B DC 4 O2 ? ? ? 1_555 BA AG . AG ? ? B DC 4 B AG 111 1_555 ? ? ? ? ? ? ? 2.365 ? ? metalc34 metalc ? ? B DG 5 O6 ? ? ? 1_555 W AG . AG ? ? B DG 5 B AG 106 1_555 ? ? ? ? ? ? ? 2.470 ? ? metalc35 metalc ? ? B DG 5 N7 ? ? ? 1_555 X AG . AG ? ? B DG 5 B AG 107 1_555 ? ? ? ? ? ? ? 2.365 ? ? metalc36 metalc ? ? B DC 6 N3 ? ? ? 1_555 S AG . AG ? ? B DC 6 B AG 102 1_555 ? ? ? ? ? ? ? 2.263 ? ? metalc37 metalc ? ? B DC 6 O2 ? ? ? 1_555 T AG . AG ? ? B DC 6 B AG 103 1_555 ? ? ? ? ? ? ? 2.530 ? ? metalc38 metalc ? ? B DG 7 N7 ? ? ? 1_555 R AG . AG ? ? B DG 7 B AG 101 1_555 ? ? ? ? ? ? ? 2.337 ? ? metalc39 metalc ? ? B DG 7 O6 ? ? ? 1_555 U AG . AG ? ? B DG 7 B AG 104 1_555 ? ? ? ? ? ? ? 2.692 ? ? metalc40 metalc ? ? B DG 9 N1 ? ? ? 1_555 T AG . AG ? ? B DG 9 B AG 103 1_555 ? ? ? ? ? ? ? 2.324 ? ? metalc41 metalc ? ? B DG 9 O6 ? ? ? 1_555 V AG . AG ? ? B DG 9 B AG 105 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc42 metalc ? ? B DC 10 N3 ? ? ? 1_555 Z AG . AG ? ? B DC 10 B AG 109 1_555 ? ? ? ? ? ? ? 2.366 ? ? metalc43 metalc ? ? B DC 10 O2 ? ? ? 1_555 BA AG . AG ? ? B DC 10 B AG 111 1_555 ? ? ? ? ? ? ? 2.465 ? ? metalc44 metalc ? ? B DC 11 N3 ? ? ? 1_555 BA AG . AG ? ? B DC 11 B AG 111 1_555 ? ? ? ? ? ? ? 2.406 ? ? metalc45 metalc ? ? B DC 11 O2 ? ? ? 1_555 DA AG . AG ? ? B DC 11 B AG 113 1_555 ? ? ? ? ? ? ? 2.357 ? ? metalc46 metalc ? ? B DG 12 N7 ? ? ? 1_555 EA AG . AG ? ? B DG 12 B AG 114 1_555 ? ? ? ? ? ? ? 2.409 ? ? metalc47 metalc ? ? B DC 13 O2 ? ? ? 1_555 CA AG . AG ? ? B DC 13 B AG 112 1_555 ? ? ? ? ? ? ? 2.593 ? ? metalc48 metalc ? ? B DC 13 N3 ? ? ? 1_555 DA AG . AG ? ? B DC 13 B AG 113 1_555 ? ? ? ? ? ? ? 2.310 ? ? metalc49 metalc ? ? B DG 14 N1 ? ? ? 1_555 Y AG . AG ? ? B DG 14 B AG 108 1_555 ? ? ? ? ? ? ? 2.372 ? ? metalc50 metalc ? ? B DG 14 O6 ? ? ? 1_555 Z AG . AG ? ? B DG 14 B AG 109 1_555 ? ? ? ? ? ? ? 2.354 ? ? metalc51 metalc ? ? B DA 15 N1 ? ? ? 1_555 V AG . AG ? ? B DA 15 B AG 105 1_555 ? ? ? ? ? ? ? 2.351 ? ? metalc52 metalc ? ? B DA 16 N1 ? ? ? 1_555 U AG . AG ? ? B DA 16 B AG 104 1_555 ? ? ? ? ? ? ? 2.269 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 A DC 4 N4 ? ? A DC 1 A DC 4 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 A DG 5 O6 ? ? A DC 1 A DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 A DG 14 N2 ? ? A DC 1 A DG 14 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog4 hydrog ? ? A DC 2 O2 ? ? ? 1_555 A DC 4 N4 ? ? A DC 2 A DC 4 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog5 hydrog ? ? A DC 4 O2 ? ? ? 1_555 A DC 11 N4 ? ? A DC 4 A DC 11 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog6 hydrog ? ? A DG 5 N7 ? ? ? 1_555 A DG 9 N2 ? ? A DG 5 A DG 9 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog7 hydrog ? ? A DC 6 O2 ? ? ? 1_555 A DG 9 N2 ? ? A DC 6 A DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog8 hydrog ? ? A DG 7 O6 ? ? ? 1_555 A DA 16 N6 ? ? A DG 7 A DA 16 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog9 hydrog ? ? A DG 9 O6 ? ? ? 1_555 A DA 15 N6 ? ? A DG 9 A DA 15 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog10 hydrog ? ? A DC 10 N4 ? ? ? 1_555 A DG 14 O6 ? ? A DC 10 A DG 14 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog11 hydrog ? ? A DC 11 O2 ? ? ? 1_555 A DC 13 N4 ? ? A DC 11 A DC 13 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog12 hydrog ? ? B DC 1 N3 ? ? ? 1_555 B DC 4 N4 ? ? B DC 1 B DC 4 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog13 hydrog ? ? B DC 1 N4 ? ? ? 1_555 B DG 5 O6 ? ? B DC 1 B DG 5 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog14 hydrog ? ? B DC 1 O2 ? ? ? 1_555 B DG 14 N2 ? ? B DC 1 B DG 14 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog15 hydrog ? ? B DC 2 O2 ? ? ? 1_555 B DC 4 N4 ? ? B DC 2 B DC 4 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog16 hydrog ? ? B DC 2 N4 ? ? ? 1_555 B DC 13 O2 ? ? B DC 2 B DC 13 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog17 hydrog ? ? B DC 4 O2 ? ? ? 1_555 B DC 11 N4 ? ? B DC 4 B DC 11 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? hydrog18 hydrog ? ? B DG 5 N7 ? ? ? 1_555 B DG 9 N2 ? ? B DG 5 B DG 9 1_555 ? ? ? ? ? ? 'DG-DG MISPAIR' ? ? ? hydrog19 hydrog ? ? B DC 6 O2 ? ? ? 1_555 B DG 9 N2 ? ? B DC 6 B DG 9 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog20 hydrog ? ? B DG 7 O6 ? ? ? 1_555 B DA 16 N6 ? ? B DG 7 B DA 16 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog21 hydrog ? ? B DG 9 O6 ? ? ? 1_555 B DA 15 N6 ? ? B DG 9 B DA 15 1_555 ? ? ? ? ? ? 'DG-DA MISPAIR' ? ? ? hydrog22 hydrog ? ? B DC 10 N4 ? ? ? 1_555 B DG 14 O6 ? ? B DC 10 B DG 14 1_555 ? ? ? ? ? ? 'DC-DG PAIR' ? ? ? hydrog23 hydrog ? ? B DC 11 O2 ? ? ? 1_555 B DC 13 N4 ? ? B DC 11 B DC 13 1_555 ? ? ? ? ? ? 'DC-DC MISPAIR' ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference metalc ? ? hydrog ? ? # 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 ? I AG . ? A AG 107 ? 1_555 N1 ? A DG 14 ? A DG 14 ? 1_555 97.5 ? 2 N3 ? A DC 1 ? A DC 1 ? 1_555 AG ? L AG . ? A AG 110 ? 1_555 O6 ? A DG 5 ? A DG 5 ? 1_555 92.2 ? 3 N3 ? A DC 2 ? A DC 2 ? 1_555 AG ? D AG . ? A AG 102 ? 1_555 O2 ? A DC 13 ? A DC 13 ? 1_555 99.6 ? 4 O2 ? A DC 2 ? A DC 2 ? 1_555 AG ? G AG . ? A AG 105 ? 1_555 N3 ? A DC 4 ? A DC 4 ? 1_555 91.9 ? 5 N7 ? A DG 3 ? A DG 3 ? 1_555 AG ? C AG . ? A AG 101 ? 1_555 N7 ? A DG 12 ? A DG 12 ? 1_555 102.4 ? 6 O2 ? A DC 4 ? A DC 4 ? 1_555 AG ? F AG . ? A AG 104 ? 1_555 O2 ? A DC 10 ? A DC 10 ? 1_555 119.6 ? 7 O2 ? A DC 4 ? A DC 4 ? 1_555 AG ? F AG . ? A AG 104 ? 1_555 N3 ? A DC 11 ? A DC 11 ? 1_555 88.9 ? 8 O2 ? A DC 10 ? A DC 10 ? 1_555 AG ? F AG . ? A AG 104 ? 1_555 N3 ? A DC 11 ? A DC 11 ? 1_555 87.0 ? 9 O2 ? A DC 6 ? A DC 6 ? 1_555 AG ? M AG . ? A AG 111 ? 1_555 N1 ? A DG 9 ? A DG 9 ? 1_555 95.4 ? 10 O6 ? A DG 7 ? A DG 7 ? 1_555 AG ? O AG . ? A AG 113 ? 1_555 N1 ? A DA 16 ? A DA 16 ? 1_555 92.0 ? 11 O6 ? A DG 9 ? A DG 9 ? 1_555 AG ? K AG . ? A AG 109 ? 1_555 N1 ? A DA 15 ? A DA 15 ? 1_555 92.1 ? 12 N3 ? A DC 10 ? A DC 10 ? 1_555 AG ? H AG . ? A AG 106 ? 1_555 O6 ? A DG 14 ? A DG 14 ? 1_555 92.6 ? 13 O2 ? A DC 11 ? A DC 11 ? 1_555 AG ? E AG . ? A AG 103 ? 1_555 N3 ? A DC 13 ? A DC 13 ? 1_555 99.3 ? 14 N3 ? B DC 1 ? B DC 1 ? 1_555 AG ? W AG . ? B AG 106 ? 1_555 O6 ? B DG 5 ? B DG 5 ? 1_555 92.2 ? 15 O2 ? B DC 1 ? B DC 1 ? 1_555 AG ? Y AG . ? B AG 108 ? 1_555 N1 ? B DG 14 ? B DG 14 ? 1_555 98.1 ? 16 O2 ? B DC 2 ? B DC 2 ? 1_555 AG ? AA AG . ? B AG 110 ? 1_555 N3 ? B DC 4 ? B DC 4 ? 1_555 90.2 ? 17 N3 ? B DC 2 ? B DC 2 ? 1_555 AG ? CA AG . ? B AG 112 ? 1_555 O2 ? B DC 13 ? B DC 13 ? 1_555 99.6 ? 18 N7 ? B DG 3 ? B DG 3 ? 1_555 AG ? EA AG . ? B AG 114 ? 1_555 N7 ? B DG 12 ? B DG 12 ? 1_555 101.1 ? 19 O2 ? B DC 4 ? B DC 4 ? 1_555 AG ? BA AG . ? B AG 111 ? 1_555 O2 ? B DC 10 ? B DC 10 ? 1_555 120.9 ? 20 O2 ? B DC 4 ? B DC 4 ? 1_555 AG ? BA AG . ? B AG 111 ? 1_555 N3 ? B DC 11 ? B DC 11 ? 1_555 90.0 ? 21 O2 ? B DC 10 ? B DC 10 ? 1_555 AG ? BA AG . ? B AG 111 ? 1_555 N3 ? B DC 11 ? B DC 11 ? 1_555 87.0 ? 22 O2 ? B DC 6 ? B DC 6 ? 1_555 AG ? T AG . ? B AG 103 ? 1_555 N1 ? B DG 9 ? B DG 9 ? 1_555 95.1 ? 23 O6 ? B DG 7 ? B DG 7 ? 1_555 AG ? U AG . ? B AG 104 ? 1_555 N1 ? B DA 16 ? B DA 16 ? 1_555 91.9 ? 24 O6 ? B DG 9 ? B DG 9 ? 1_555 AG ? V AG . ? B AG 105 ? 1_555 N1 ? B DA 15 ? B DA 15 ? 1_555 92.1 ? 25 N3 ? B DC 10 ? B DC 10 ? 1_555 AG ? Z AG . ? B AG 109 ? 1_555 O6 ? B DG 14 ? B DG 14 ? 1_555 91.5 ? 26 O2 ? B DC 11 ? B DC 11 ? 1_555 AG ? DA AG . ? B AG 113 ? 1_555 N3 ? B DC 13 ? B DC 13 ? 1_555 99.0 ? # _pdbx_entry_details.entry_id 9KHW _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 _pdbx_entry_details.has_protein_modification 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 CL CL CL N N 2 DA OP3 O N N 3 DA P P N N 4 DA OP1 O N N 5 DA OP2 O N N 6 DA "O5'" O N N 7 DA "C5'" C N N 8 DA "C4'" C N R 9 DA "O4'" O N N 10 DA "C3'" C N S 11 DA "O3'" O N N 12 DA "C2'" C N N 13 DA "C1'" C N R 14 DA N9 N Y N 15 DA C8 C Y N 16 DA N7 N Y N 17 DA C5 C Y N 18 DA C6 C Y N 19 DA N6 N N N 20 DA N1 N Y N 21 DA C2 C Y N 22 DA N3 N Y N 23 DA C4 C Y N 24 DA HOP3 H N N 25 DA HOP2 H N N 26 DA "H5'" H N N 27 DA "H5''" H N N 28 DA "H4'" H N N 29 DA "H3'" H N N 30 DA "HO3'" H N N 31 DA "H2'" H N N 32 DA "H2''" H N N 33 DA "H1'" H N N 34 DA H8 H N N 35 DA H61 H N N 36 DA H62 H N N 37 DA H2 H N N 38 DC OP3 O N N 39 DC P P N N 40 DC OP1 O N N 41 DC OP2 O N N 42 DC "O5'" O N N 43 DC "C5'" C N N 44 DC "C4'" C N R 45 DC "O4'" O N N 46 DC "C3'" C N S 47 DC "O3'" O N N 48 DC "C2'" C N N 49 DC "C1'" C N R 50 DC N1 N N N 51 DC C2 C N N 52 DC O2 O N N 53 DC N3 N N N 54 DC C4 C N N 55 DC N4 N N N 56 DC C5 C N N 57 DC C6 C N N 58 DC HOP3 H N N 59 DC HOP2 H N N 60 DC "H5'" H N N 61 DC "H5''" H N N 62 DC "H4'" H N N 63 DC "H3'" H N N 64 DC "HO3'" H N N 65 DC "H2'" H N N 66 DC "H2''" H N N 67 DC "H1'" H N N 68 DC H41 H N N 69 DC H42 H N N 70 DC H5 H N N 71 DC H6 H N N 72 DG OP3 O N N 73 DG P P N N 74 DG OP1 O N N 75 DG OP2 O N N 76 DG "O5'" O N N 77 DG "C5'" C N N 78 DG "C4'" C N R 79 DG "O4'" O N N 80 DG "C3'" C N S 81 DG "O3'" O N N 82 DG "C2'" C N N 83 DG "C1'" C N R 84 DG N9 N Y N 85 DG C8 C Y N 86 DG N7 N Y N 87 DG C5 C Y N 88 DG C6 C N N 89 DG O6 O N N 90 DG N1 N N N 91 DG C2 C N N 92 DG N2 N N N 93 DG N3 N N N 94 DG C4 C Y N 95 DG HOP3 H N N 96 DG HOP2 H N N 97 DG "H5'" H N N 98 DG "H5''" H N N 99 DG "H4'" H N N 100 DG "H3'" H N N 101 DG "HO3'" H N N 102 DG "H2'" H N N 103 DG "H2''" H N N 104 DG "H1'" H N N 105 DG H8 H N N 106 DG H1 H N N 107 DG H21 H N N 108 DG H22 H N N 109 HOH O O N N 110 HOH H1 H N N 111 HOH H2 H N N 112 # 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 HOH O H1 sing N N 113 HOH O H2 sing N N 114 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 9KHW 'double helix' 9KHW 'mismatched base pair' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 4 1_555 A DC 11 1_555 1.614 -3.371 -0.470 -9.268 37.689 -82.521 1 A_DC4:DC11_A A 4 ? A 11 ? ? ? 1 A DG 5 1_555 A DC 1 1_555 0.049 -3.072 0.239 -25.985 -6.215 148.192 2 A_DG5:DC1_A A 5 ? A 1 ? ? ? 1 A DG 9 1_555 A DA 15 1_555 -2.120 3.185 -0.212 -0.964 -5.322 -114.814 3 A_DG9:DA15_A A 9 ? A 15 ? ? 4 1 A DA 16 1_555 A DG 7 1_555 0.896 3.860 0.350 -18.733 -19.336 -162.946 4 A_DA16:DG7_A A 16 ? A 7 ? ? ? 1 B DG 7 1_555 B DA 16 1_555 -0.852 -3.923 -0.296 18.546 19.210 162.875 5 B_DG7:DA16_B B 7 ? B 16 ? ? ? 1 B DG 9 1_555 B DA 15 1_555 -2.110 3.195 -0.238 -0.816 -5.480 -114.862 6 B_DG9:DA15_B B 9 ? B 15 ? ? 4 1 B DC 10 1_555 B DG 14 1_555 1.343 1.892 0.005 0.082 5.184 -97.452 7 B_DC10:DG14_B B 10 ? B 14 ? ? ? 1 B DC 2 1_555 B DC 13 1_555 -0.944 3.271 2.496 -18.703 -1.363 96.927 8 B_DC2:DC13_B B 2 ? B 13 ? ? ? # 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 4 1_555 A DC 11 1_555 A DG 5 1_555 A DC 1 1_555 2.087 -2.747 -1.617 -147.831 63.788 76.779 -0.909 0.051 -3.355 33.307 77.190 165.139 1 AA_DC4DG5:DC1DC11_AA A 4 ? A 11 ? A 5 ? A 1 ? 1 A DG 5 1_555 A DC 1 1_555 A DG 9 1_555 A DA 15 1_555 2.335 5.334 -1.918 -14.145 -5.471 106.121 3.273 -1.332 -2.314 -3.411 8.820 106.872 2 AA_DG5DG9:DA15DC1_AA A 5 ? A 1 ? A 9 ? A 15 ? 1 A DA 16 1_555 A DG 7 1_555 B DG 7 1_555 B DA 16 1_555 -2.965 -2.484 0.105 -140.151 105.237 -169.094 1.240 -1.485 0.021 -52.625 -70.084 -179.550 3 AB_DA16DG7:DA16DG7_BA A 16 ? A 7 ? B 7 ? B 16 ? 1 B DG 7 1_555 B DA 16 1_555 B DG 9 1_555 B DA 15 1_555 -0.201 3.222 0.436 -150.668 83.223 80.684 1.385 -0.312 1.603 42.282 76.547 173.999 4 BB_DG7DG9:DA15DA16_BB B 7 ? B 16 ? B 9 ? B 15 ? 1 B DG 9 1_555 B DA 15 1_555 B DC 10 1_555 B DG 14 1_555 -0.023 -1.617 3.239 -0.038 -3.387 38.102 -2.038 0.030 3.365 -5.176 0.058 38.247 5 BB_DG9DC10:DG14DA15_BB B 9 ? B 15 ? B 10 ? B 14 ? 1 B DC 10 1_555 B DG 14 1_555 B DC 2 1_555 B DC 13 1_555 0.293 2.425 -0.674 161.276 -21.774 -30.557 -1.268 -0.165 -0.147 11.735 86.921 -163.354 6 BB_DC10DC2:DC13DG14_BB B 10 ? B 14 ? B 2 ? B 13 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Novo Nordisk Foundation' Denmark NNF22OC0073734 1 'Independent Research Fund Denmark - Technology and Production Sciences' Denmark 0136-00024B 2 'Independent Research Fund Denmark - Technology and Production Sciences' Denmark 3103-00279B 3 'Marie Sklodowska-Curie Actions, FragNET ITN' 'European Union' 'NIR-emitting Ag-DNAs 101151897' 4 'Japan Agency for Medical Research and Development (AMED)' Japan JP24ama121014 5 # loop_ _pdbx_serial_crystallography_sample_delivery.diffrn_id _pdbx_serial_crystallography_sample_delivery.description _pdbx_serial_crystallography_sample_delivery.method 1 ? 'fixed target' 2 ? 'fixed target' # _atom_sites.entry_id 9KHW _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.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.036744 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008937 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.018807 _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] 0.037816 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol AG C CL N O P # loop_ #