data_5WKD # _entry.id 5WKD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _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 5WKD pdb_00005wkd 10.2210/pdb5wkd/pdb WWPDB D_1000229073 ? ? # 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 2018-04-18 2 'Structure model' 1 1 2018-05-30 3 'Structure model' 1 2 2018-06-06 4 'Structure model' 1 3 2018-06-20 5 'Structure model' 1 4 2019-02-20 6 'Structure model' 1 5 2019-12-18 7 'Structure model' 1 6 2024-03-13 8 'Structure model' 1 7 2024-04-03 # _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' 'Data collection' 2 2 'Structure model' 'Database references' 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Database references' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Database references' 7 5 'Structure model' 'Author supporting evidence' 8 5 'Structure model' 'Data collection' 9 6 'Structure model' 'Author supporting evidence' 10 7 'Structure model' 'Data collection' 11 7 'Structure model' 'Database references' 12 8 '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' citation 4 4 'Structure model' citation 5 5 'Structure model' pdbx_audit_support 6 6 'Structure model' pdbx_audit_support 7 7 'Structure model' chem_comp_atom 8 7 'Structure model' chem_comp_bond 9 7 'Structure model' database_2 10 8 '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_id_CSD' 4 2 'Structure model' '_citation.journal_id_ISSN' 5 2 'Structure model' '_citation.pdbx_database_id_DOI' 6 2 'Structure model' '_citation.title' 7 2 'Structure model' '_citation.year' 8 3 'Structure model' '_citation.journal_abbrev' 9 3 'Structure model' '_citation.pdbx_database_id_PubMed' 10 3 'Structure model' '_citation.title' 11 4 'Structure model' '_citation.journal_volume' 12 4 'Structure model' '_citation.page_first' 13 4 'Structure model' '_citation.page_last' 14 5 'Structure model' '_pdbx_audit_support.funding_organization' 15 6 'Structure model' '_pdbx_audit_support.funding_organization' 16 7 'Structure model' '_database_2.pdbx_DOI' 17 7 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5WKD _pdbx_database_status.recvd_initial_deposition_date 2017-07-25 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Guenther, E.L.' 1 ? 'Trinh, H.' 2 ? 'Sawaya, M.R.' 3 ? 'Cascio, D.' 4 ? 'Eisenberg, D.S.' 5 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat. Struct. Mol. Biol.' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1545-9985 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 25 _citation.language ? _citation.page_first 463 _citation.page_last 471 _citation.title 'Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41594-018-0064-2 _citation.pdbx_database_id_PubMed 29786080 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Guenther, E.L.' 1 ? primary 'Cao, Q.' 2 ? primary 'Trinh, H.' 3 ? primary 'Lu, J.' 4 ? primary 'Sawaya, M.R.' 5 ? primary 'Cascio, D.' 6 ? primary 'Boyer, D.R.' 7 ? primary 'Rodriguez, J.A.' 8 ? primary 'Hughes, M.P.' 9 ? primary 'Eisenberg, D.S.' 10 ? # 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 'TAR DNA-binding protein 43' 689.634 1 ? ? 'UNP residues 300-306' ? 2 water nat water 18.015 2 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name TDP-43 # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GNNQGSN _entity_poly.pdbx_seq_one_letter_code_can GNNQGSN _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 ASN n 1 3 ASN n 1 4 GLN n 1 5 GLY n 1 6 SER n 1 7 ASN 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 7 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name Human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # 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 GLY 1 300 1 GLY GLY A . n A 1 2 ASN 2 301 2 ASN ASN A . n A 1 3 ASN 3 302 3 ASN ASN A . n A 1 4 GLN 4 303 4 GLN GLN A . n A 1 5 GLY 5 304 5 GLY GLY A . n A 1 6 SER 6 305 6 SER SER A . n A 1 7 ASN 7 306 7 ASN ASN A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 HOH 1 401 1 HOH HOH A . B 2 HOH 2 402 2 HOH HOH A . # 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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? . 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALEPACK ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.22 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DENZO ? ? ? . 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? . 5 # _cell.length_a 50.347 _cell.length_b 4.777 _cell.length_c 14.746 _cell.angle_alpha 90.000 _cell.angle_beta 101.730 _cell.angle_gamma 90.000 _cell.entry_id 5WKD _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.entry_id 5WKD _symmetry.Int_Tables_number 5 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? # _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 5WKD _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 1.26 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 2.45 _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 7.5 _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details '100mM Bis-Tris propane, pH 7.5, 200 mM sodium sulfate, 20% PEG3350' _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_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-08-13 # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si(220)' _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 0.9791 _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 'APS BEAMLINE 24-ID-E' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9791 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 24-ID-E _diffrn_source.pdbx_synchrotron_site APS # _reflns.entry_id 5WKD _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 100.000 _reflns.d_resolution_high 1.800 _reflns.number_obs 373 _reflns.number_all ? _reflns.percent_possible_obs 91.600 _reflns.pdbx_Rmerge_I_obs 0.158 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 5.400 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 2.300 _reflns.pdbx_Rrim_I_all ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_CC_half ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_number_measured_all 845 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_chi_squared 2.003 _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.observed_criterion_I_max ? _reflns.observed_criterion_I_min ? _reflns.pdbx_d_res_high_opt ? _reflns.pdbx_d_res_low_opt ? _reflns.details ? # loop_ _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.pdbx_rejects _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_CC_half 1 1 1.800 1.860 ? ? 28 ? 0.250 ? ? 2.711 2.200 ? ? ? ? ? ? ? ? 84.800 ? ? ? 1 2 1.860 1.940 ? ? 39 ? 0.254 ? ? 3.034 2.400 ? ? ? ? ? ? ? ? 88.600 ? ? ? 1 3 1.940 2.030 ? ? 36 ? 0.316 ? ? 2.952 2.200 ? ? ? ? ? ? ? ? 92.300 ? ? ? 1 4 2.030 2.130 ? ? 33 ? 0.164 ? ? 1.670 2.400 ? ? ? ? ? ? ? ? 97.100 ? ? ? 1 5 2.130 2.270 ? ? 45 ? 0.285 ? ? 2.188 2.300 ? ? ? ? ? ? ? ? 90.000 ? ? ? 1 6 2.270 2.440 ? ? 35 ? 0.242 ? ? 2.095 2.000 ? ? ? ? ? ? ? ? 89.700 ? ? ? 1 7 2.440 2.690 ? ? 35 ? 0.175 ? ? 1.611 2.500 ? ? ? ? ? ? ? ? 94.600 ? ? ? 1 8 2.690 3.080 ? ? 36 ? 0.111 ? ? 1.492 2.500 ? ? ? ? ? ? ? ? 92.300 ? ? ? 1 9 3.080 3.880 ? ? 41 ? 0.125 ? ? 0.818 2.400 ? ? ? ? ? ? ? ? 97.600 ? ? ? 1 10 3.880 100.000 ? ? 45 ? 0.075 ? ? 1.906 2.000 ? ? ? ? ? ? ? ? 90.000 ? ? ? # _refine.entry_id 5WKD _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.8000 _refine.ls_d_res_low 24.6500 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 90.3900 _refine.ls_number_reflns_obs 345 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1843 _refine.ls_R_factor_R_work 0.1837 _refine.ls_wR_factor_R_work 0.1674 _refine.ls_R_factor_R_free 0.1949 _refine.ls_wR_factor_R_free 0.1803 _refine.ls_percent_reflns_R_free 6.0000 _refine.ls_number_reflns_R_free 22 _refine.ls_number_reflns_R_work ? _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 8.8260 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.1600 _refine.aniso_B[2][2] -0.2400 _refine.aniso_B[3][3] 0.3200 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.1400 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9610 _refine.correlation_coeff_Fo_to_Fc_free 0.9500 _refine.overall_SU_R_Cruickshank_DPI 0.2052 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.overall_SU_R_free 0.1412 _refine.pdbx_overall_ESU_R 0.2050 _refine.pdbx_overall_ESU_R_Free 0.1410 _refine.overall_SU_ML 0.1140 _refine.overall_SU_B 3.9150 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'idealized beta strand' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8177 _refine.B_iso_max 24.530 _refine.B_iso_min 4.440 _refine.pdbx_overall_phase_error ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_R_factor_R_free_error_details ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.8000 _refine_hist.d_res_low 24.6500 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 50 _refine_hist.pdbx_number_residues_total 7 _refine_hist.pdbx_B_iso_mean_solvent 16.87 _refine_hist.pdbx_number_atoms_protein 48 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'X-RAY DIFFRACTION' r_bond_refined_d 47 0.021 0.019 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 30 0.020 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 62 1.804 1.873 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 73 0.838 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 6 4.310 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 4 61.302 30.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 6 6.174 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 5 0.097 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 62 0.008 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 6 0.000 0.020 ? ? # _refine_ls_shell.d_res_high 1.8020 _refine_ls_shell.d_res_low 1.8490 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 70.5900 _refine_ls_shell.number_reflns_R_work 23 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2930 _refine_ls_shell.R_factor_R_free 0.4030 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 1 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.number_reflns_all 24 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 5WKD _struct.title 'Crystal structure of the segment, GNNQGSN, from the low complexity domain of TDP-43, residues 300-306' _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 5WKD _struct_keywords.text 'TDP-43, amyloid, low complexity domain, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TADBP_HUMAN _struct_ref.pdbx_db_accession Q13148 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GNNQGSN _struct_ref.pdbx_align_begin 300 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 5WKD _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 7 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q13148 _struct_ref_seq.db_align_beg 300 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 306 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 300 _struct_ref_seq.pdbx_auth_seq_align_end 306 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B 1 2 A,B 1 3 A,B 1 4 A,B 1 5 A,B 1 6 A,B 1 7 A,B 1 8 A,B 1 9 A,B 1 10 A,B # _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 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4.7770000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_575 x,y+2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9.5540000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_545 x,y-1,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -4.7770000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 1_535 x,y-2,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -9.5540000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 4_555 -x+1/2,y+1/2,-z -1.0000000000 0.0000000000 0.0000000000 25.1735000000 0.0000000000 1.0000000000 0.0000000000 2.3885000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 7 'crystal symmetry operation' 4_565 -x+1/2,y+3/2,-z -1.0000000000 0.0000000000 0.0000000000 25.1735000000 0.0000000000 1.0000000000 0.0000000000 7.1655000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 8 'crystal symmetry operation' 4_575 -x+1/2,y+5/2,-z -1.0000000000 0.0000000000 0.0000000000 25.1735000000 0.0000000000 1.0000000000 0.0000000000 11.9425000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 9 'crystal symmetry operation' 4_545 -x+1/2,y-1/2,-z -1.0000000000 0.0000000000 0.0000000000 25.1735000000 0.0000000000 1.0000000000 0.0000000000 -2.3885000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 10 'crystal symmetry operation' 4_535 -x+1/2,y-3/2,-z -1.0000000000 0.0000000000 0.0000000000 25.1735000000 0.0000000000 1.0000000000 0.0000000000 -7.1655000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id A _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 401 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id B _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 ASN N N N N 1 ASN CA C N S 2 ASN C C N N 3 ASN O O N N 4 ASN CB C N N 5 ASN CG C N N 6 ASN OD1 O N N 7 ASN ND2 N N N 8 ASN OXT O N N 9 ASN H H N N 10 ASN H2 H N N 11 ASN HA H N N 12 ASN HB2 H N N 13 ASN HB3 H N N 14 ASN HD21 H N N 15 ASN HD22 H N N 16 ASN HXT H N N 17 GLN N N N N 18 GLN CA C N S 19 GLN C C N N 20 GLN O O N N 21 GLN CB C N N 22 GLN CG C N N 23 GLN CD C N N 24 GLN OE1 O N N 25 GLN NE2 N N N 26 GLN OXT O N N 27 GLN H H N N 28 GLN H2 H N N 29 GLN HA H N N 30 GLN HB2 H N N 31 GLN HB3 H N N 32 GLN HG2 H N N 33 GLN HG3 H N N 34 GLN HE21 H N N 35 GLN HE22 H N N 36 GLN HXT H N N 37 GLY N N N N 38 GLY CA C N N 39 GLY C C N N 40 GLY O O N N 41 GLY OXT O N N 42 GLY H H N N 43 GLY H2 H N N 44 GLY HA2 H N N 45 GLY HA3 H N N 46 GLY HXT H N N 47 HOH O O N N 48 HOH H1 H N N 49 HOH H2 H N N 50 SER N N N N 51 SER CA C N S 52 SER C C N N 53 SER O O N N 54 SER CB C N N 55 SER OG O N N 56 SER OXT O N N 57 SER H H N N 58 SER H2 H N N 59 SER HA H N N 60 SER HB2 H N N 61 SER HB3 H N N 62 SER HG H N N 63 SER HXT H N N 64 # 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 ASN N CA sing N N 1 ASN N H sing N N 2 ASN N H2 sing N N 3 ASN CA C sing N N 4 ASN CA CB sing N N 5 ASN CA HA sing N N 6 ASN C O doub N N 7 ASN C OXT sing N N 8 ASN CB CG sing N N 9 ASN CB HB2 sing N N 10 ASN CB HB3 sing N N 11 ASN CG OD1 doub N N 12 ASN CG ND2 sing N N 13 ASN ND2 HD21 sing N N 14 ASN ND2 HD22 sing N N 15 ASN OXT HXT sing N N 16 GLN N CA sing N N 17 GLN N H sing N N 18 GLN N H2 sing N N 19 GLN CA C sing N N 20 GLN CA CB sing N N 21 GLN CA HA sing N N 22 GLN C O doub N N 23 GLN C OXT sing N N 24 GLN CB CG sing N N 25 GLN CB HB2 sing N N 26 GLN CB HB3 sing N N 27 GLN CG CD sing N N 28 GLN CG HG2 sing N N 29 GLN CG HG3 sing N N 30 GLN CD OE1 doub N N 31 GLN CD NE2 sing N N 32 GLN NE2 HE21 sing N N 33 GLN NE2 HE22 sing N N 34 GLN OXT HXT sing N N 35 GLY N CA sing N N 36 GLY N H sing N N 37 GLY N H2 sing N N 38 GLY CA C sing N N 39 GLY CA HA2 sing N N 40 GLY CA HA3 sing N N 41 GLY C O doub N N 42 GLY C OXT sing N N 43 GLY OXT HXT sing N N 44 HOH O H1 sing N N 45 HOH O H2 sing N N 46 SER N CA sing N N 47 SER N H sing N N 48 SER N H2 sing N N 49 SER CA C sing N N 50 SER CA CB sing N N 51 SER CA HA sing N N 52 SER C O doub N N 53 SER C OXT sing N N 54 SER CB OG sing N N 55 SER CB HB2 sing N N 56 SER CB HB3 sing N N 57 SER OG HG sing N N 58 SER OXT HXT sing N N 59 # _pdbx_audit_support.funding_organization 'National Institutes of Health/National Institute on Aging (NIH/NIA)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number 'NIH NIA AG029430' _pdbx_audit_support.ordinal 1 # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'in silico model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details 'idealized beta strand' # _atom_sites.entry_id 5WKD _atom_sites.fract_transf_matrix[1][1] 0.019862 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.004125 _atom_sites.fract_transf_matrix[2][1] -0.000000 _atom_sites.fract_transf_matrix[2][2] 0.209336 _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] 0.069262 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O # loop_