data_5WMJ # _entry.id 5WMJ # _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 5WMJ pdb_00005wmj 10.2210/pdb5wmj/pdb WWPDB D_1000229292 ? ? # 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 2018-03-28 2 'Structure model' 1 1 2018-07-18 3 'Structure model' 1 2 2019-11-06 4 'Structure model' 1 3 2019-11-20 5 'Structure model' 1 4 2024-03-13 6 'Structure model' 1 5 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' 'Author supporting evidence' 4 3 'Structure model' 'Data collection' 5 4 'Structure model' 'Author supporting evidence' 6 5 'Structure model' 'Data collection' 7 5 'Structure model' 'Database references' 8 6 '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 3 'Structure model' pdbx_audit_support 3 4 'Structure model' pdbx_audit_support 4 5 'Structure model' chem_comp_atom 5 5 'Structure model' chem_comp_bond 6 5 'Structure model' database_2 7 6 '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.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 3 'Structure model' '_pdbx_audit_support.funding_organization' 5 3 'Structure model' '_pdbx_audit_support.grant_number' 6 4 'Structure model' '_pdbx_audit_support.funding_organization' 7 5 'Structure model' '_database_2.pdbx_DOI' 8 5 '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 5WMJ _pdbx_database_status.recvd_initial_deposition_date 2017-07-28 _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 'Sangwan, S.' 1 ? 'Sawaya, M.' 2 ? 'Eisenberg, D.' 3 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Protein Sci.' _citation.journal_id_ASTM PRCIEI _citation.journal_id_CSD 0795 _citation.journal_id_ISSN 1469-896X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 27 _citation.language ? _citation.page_first 1231 _citation.page_last 1242 _citation.title 'Atomic structures of corkscrew-forming segments of SOD1 reveal varied oligomer conformations.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/pro.3391 _citation.pdbx_database_id_PubMed 29453800 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Sangwan, S.' 1 ? primary 'Sawaya, M.R.' 2 ? primary 'Murray, K.A.' 3 ? primary 'Hughes, M.P.' 4 ? primary 'Eisenberg, D.S.' 5 ? # 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 'Superoxide dismutase [Cu-Zn]' 689.823 2 1.15.1.1 ? 'UNP residues 31-36' ? 2 non-polymer syn 'trifluoroacetic acid' 114.023 1 ? ? ? ? 3 water nat water 18.015 6 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Superoxide dismutase 1,hSod1' # _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 KVWGSI _entity_poly.pdbx_seq_one_letter_code_can KVWGSI _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 'trifluoroacetic acid' TFA 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LYS n 1 2 VAL n 1 3 TRP n 1 4 GLY n 1 5 SER n 1 6 ILE 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 6 _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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TFA non-polymer . 'trifluoroacetic acid' ? 'C2 H F3 O2' 114.023 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # 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 LYS 1 1 1 LYS LYS A . n A 1 2 VAL 2 2 2 VAL VAL A . n A 1 3 TRP 3 3 3 TRP TRP A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 SER 5 5 5 SER SER A . n A 1 6 ILE 6 6 6 ILE ILE A . n B 1 1 LYS 1 1 1 LYS LYS B . n B 1 2 VAL 2 2 2 VAL VAL B . n B 1 3 TRP 3 3 3 TRP TRP B . n B 1 4 GLY 4 4 4 GLY GLY B . n B 1 5 SER 5 5 5 SER SER B . n B 1 6 ILE 6 6 6 ILE ILE B . 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 C 2 TFA 1 101 101 TFA TFA B . D 3 HOH 1 101 102 HOH HOH A . D 3 HOH 2 102 101 HOH HOH A . E 3 HOH 1 201 201 HOH HOH B . E 3 HOH 2 202 203 HOH HOH B . E 3 HOH 3 203 202 HOH HOH B . E 3 HOH 4 204 204 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 ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? . 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DENZO ? ? ? . 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALEPACK ? ? ? 1.98.7 3 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 2.52 4 # _cell.length_a 9.518 _cell.length_b 20.282 _cell.length_c 44.249 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 5WMJ _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.entry_id 5WMJ _symmetry.Int_Tables_number 19 _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 5WMJ _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 1.55 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 20.54 _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 _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 'Reservoir solution contained 4M Sodium Formate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 298 _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 2013-06-06 # _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 0.9791 _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 5WMJ _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 1.400 _reflns.number_obs 1738 _reflns.number_all ? _reflns.percent_possible_obs 89.600 _reflns.pdbx_Rmerge_I_obs 0.166 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 4.600 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.700 _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 11623 _reflns.pdbx_scaling_rejects ? _reflns.pdbx_chi_squared 1.012 _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 1.400 1.450 ? ? 132 ? 0.550 ? ? 0.986 3.100 ? ? ? ? ? ? ? ? 75.000 ? ? ? 1 2 1.450 1.510 ? ? 141 ? 0.478 ? ? 0.705 3.000 ? ? ? ? ? ? ? ? 77.000 ? ? ? 1 3 1.510 1.580 ? ? 168 ? 0.503 ? ? 0.873 5.000 ? ? ? ? ? ? ? ? 84.400 ? ? ? 1 4 1.580 1.660 ? ? 165 ? 0.426 ? ? 0.816 6.100 ? ? ? ? ? ? ? ? 91.200 ? ? ? 1 5 1.660 1.760 ? ? 170 ? 0.376 ? ? 0.732 6.200 ? ? ? ? ? ? ? ? 95.000 ? ? ? 1 6 1.760 1.900 ? ? 182 ? 0.328 ? ? 0.853 8.000 ? ? ? ? ? ? ? ? 89.200 ? ? ? 1 7 1.900 2.090 ? ? 173 ? 0.182 ? ? 1.093 9.000 ? ? ? ? ? ? ? ? 94.500 ? ? ? 1 8 2.090 2.390 ? ? 187 ? 0.159 ? ? 1.147 8.600 ? ? ? ? ? ? ? ? 93.500 ? ? ? 1 9 2.390 3.020 ? ? 193 ? 0.156 ? ? 1.092 8.400 ? ? ? ? ? ? ? ? 96.500 ? ? ? 1 10 3.020 100.000 ? ? 227 ? 0.079 ? ? 1.282 7.200 ? ? ? ? ? ? ? ? 97.000 ? ? ? # _refine.entry_id 5WMJ _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.4000 _refine.ls_d_res_low 22.1200 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 89.3100 _refine.ls_number_reflns_obs 1564 _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 U VALUES : REFINED INDIVIDUALLY' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1706 _refine.ls_R_factor_R_work 0.1707 _refine.ls_wR_factor_R_work 0.1474 _refine.ls_R_factor_R_free 0.1698 _refine.ls_wR_factor_R_free 0.1566 _refine.ls_percent_reflns_R_free 9.1000 _refine.ls_number_reflns_R_free 157 _refine.ls_number_reflns_R_work ? _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 5.3990 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.0100 _refine.aniso_B[2][2] 0.3400 _refine.aniso_B[3][3] -0.3500 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.0000 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9700 _refine.correlation_coeff_Fo_to_Fc_free 0.9710 _refine.overall_SU_R_Cruickshank_DPI 0.0866 _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 0.0714 _refine.pdbx_overall_ESU_R 0.0870 _refine.pdbx_overall_ESU_R_Free 0.0710 _refine.overall_SU_ML 0.0470 _refine.overall_SU_B 1.2600 _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 '2 ANTI-PARALLEL BETA STRANDS' _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 0.8693 _refine.B_iso_max 26.040 _refine.B_iso_min 2.080 _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 1.4000 _refine_hist.d_res_low 22.1200 _refine_hist.pdbx_number_atoms_ligand 7 _refine_hist.number_atoms_solvent 7 _refine_hist.number_atoms_total 112 _refine_hist.pdbx_number_residues_total 12 _refine_hist.pdbx_B_iso_mean_ligand 12.58 _refine_hist.pdbx_B_iso_mean_solvent 17.75 _refine_hist.pdbx_number_atoms_protein 98 _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 120 0.020 0.020 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 111 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 165 2.002 1.913 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 253 0.629 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 12 5.078 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_2_deg 3 6.210 20.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 19 9.800 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 16 0.196 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 119 0.013 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 29 0.000 0.020 ? ? # _refine_ls_shell.d_res_high 1.3980 _refine_ls_shell.d_res_low 1.4340 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 64.5700 _refine_ls_shell.number_reflns_R_work 77 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2800 _refine_ls_shell.R_factor_R_free 0.2530 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 5 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.number_reflns_all 82 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _struct.entry_id 5WMJ _struct.title 'KVWGSI segment from Superoxide Dismutase 1,residues 30-35' _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 5WMJ _struct_keywords.text 'Amyloid Fibril, 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 1 ? C N N 2 ? D N N 3 ? E N N 3 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code SODC_HUMAN _struct_ref.pdbx_db_accession P00441 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KVWGSI _struct_ref.pdbx_align_begin 31 # 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 5WMJ A 1 ? 6 ? P00441 31 ? 36 ? 1 6 2 1 5WMJ B 1 ? 6 ? P00441 31 ? 36 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2,3,4 A,D 1 1,2,5,6 B,C,E # _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_655 x+1,y,z 1.0000000000 0.0000000000 0.0000000000 9.5180000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 4_545 x+1/2,-y-1/2,-z 1.0000000000 0.0000000000 0.0000000000 4.7590000000 0.0000000000 -1.0000000000 0.0000000000 -10.1410000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_645 x+3/2,-y-1/2,-z 1.0000000000 0.0000000000 0.0000000000 14.2770000000 0.0000000000 -1.0000000000 0.0000000000 -10.1410000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 5 'crystal symmetry operation' 4_535 x+1/2,-y-3/2,-z 1.0000000000 0.0000000000 0.0000000000 4.7590000000 0.0000000000 -1.0000000000 0.0000000000 -30.4230000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 6 'crystal symmetry operation' 4_635 x+3/2,-y-3/2,-z 1.0000000000 0.0000000000 0.0000000000 14.2770000000 0.0000000000 -1.0000000000 0.0000000000 -30.4230000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id B _struct_site.pdbx_auth_comp_id TFA _struct_site.pdbx_auth_seq_id 101 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 12 _struct_site.details 'binding site for residue TFA B 101' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 12 LYS A 1 ? LYS A 1 . ? 1_455 ? 2 AC1 12 LYS A 1 ? LYS A 1 . ? 1_555 ? 3 AC1 12 VAL A 2 ? VAL A 2 . ? 1_455 ? 4 AC1 12 TRP A 3 ? TRP A 3 . ? 1_555 ? 5 AC1 12 TRP A 3 ? TRP A 3 . ? 1_455 ? 6 AC1 12 GLY A 4 ? GLY A 4 . ? 4_445 ? 7 AC1 12 SER A 5 ? SER A 5 . ? 4_445 ? 8 AC1 12 ILE A 6 ? ILE A 6 . ? 4_445 ? 9 AC1 12 HOH D . ? HOH A 101 . ? 1_555 ? 10 AC1 12 VAL B 2 ? VAL B 2 . ? 4_435 ? 11 AC1 12 SER B 5 ? SER B 5 . ? 1_555 ? 12 AC1 12 HOH E . ? HOH B 203 . ? 1_555 ? # 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 GLY N N N N 1 GLY CA C N N 2 GLY C C N N 3 GLY O O N N 4 GLY OXT O N N 5 GLY H H N N 6 GLY H2 H N N 7 GLY HA2 H N N 8 GLY HA3 H N N 9 GLY HXT H N N 10 HOH O O N N 11 HOH H1 H N N 12 HOH H2 H N N 13 ILE N N N N 14 ILE CA C N S 15 ILE C C N N 16 ILE O O N N 17 ILE CB C N S 18 ILE CG1 C N N 19 ILE CG2 C N N 20 ILE CD1 C N N 21 ILE OXT O N N 22 ILE H H N N 23 ILE H2 H N N 24 ILE HA H N N 25 ILE HB H N N 26 ILE HG12 H N N 27 ILE HG13 H N N 28 ILE HG21 H N N 29 ILE HG22 H N N 30 ILE HG23 H N N 31 ILE HD11 H N N 32 ILE HD12 H N N 33 ILE HD13 H N N 34 ILE HXT H N N 35 LYS N N N N 36 LYS CA C N S 37 LYS C C N N 38 LYS O O N N 39 LYS CB C N N 40 LYS CG C N N 41 LYS CD C N N 42 LYS CE C N N 43 LYS NZ N N N 44 LYS OXT O N N 45 LYS H H N N 46 LYS H2 H N N 47 LYS HA H N N 48 LYS HB2 H N N 49 LYS HB3 H N N 50 LYS HG2 H N N 51 LYS HG3 H N N 52 LYS HD2 H N N 53 LYS HD3 H N N 54 LYS HE2 H N N 55 LYS HE3 H N N 56 LYS HZ1 H N N 57 LYS HZ2 H N N 58 LYS HZ3 H N N 59 LYS HXT H N N 60 SER N N N N 61 SER CA C N S 62 SER C C N N 63 SER O O N N 64 SER CB C N N 65 SER OG O N N 66 SER OXT O N N 67 SER H H N N 68 SER H2 H N N 69 SER HA H N N 70 SER HB2 H N N 71 SER HB3 H N N 72 SER HG H N N 73 SER HXT H N N 74 TFA C1 C N N 75 TFA C2 C N N 76 TFA O O N N 77 TFA F1 F N N 78 TFA F2 F N N 79 TFA F3 F N N 80 TFA OXT O N N 81 TFA HXT H N N 82 TRP N N N N 83 TRP CA C N S 84 TRP C C N N 85 TRP O O N N 86 TRP CB C N N 87 TRP CG C Y N 88 TRP CD1 C Y N 89 TRP CD2 C Y N 90 TRP NE1 N Y N 91 TRP CE2 C Y N 92 TRP CE3 C Y N 93 TRP CZ2 C Y N 94 TRP CZ3 C Y N 95 TRP CH2 C Y N 96 TRP OXT O N N 97 TRP H H N N 98 TRP H2 H N N 99 TRP HA H N N 100 TRP HB2 H N N 101 TRP HB3 H N N 102 TRP HD1 H N N 103 TRP HE1 H N N 104 TRP HE3 H N N 105 TRP HZ2 H N N 106 TRP HZ3 H N N 107 TRP HH2 H N N 108 TRP HXT H N N 109 VAL N N N N 110 VAL CA C N S 111 VAL C C N N 112 VAL O O N N 113 VAL CB C N N 114 VAL CG1 C N N 115 VAL CG2 C N N 116 VAL OXT O N N 117 VAL H H N N 118 VAL H2 H N N 119 VAL HA H N N 120 VAL HB H N N 121 VAL HG11 H N N 122 VAL HG12 H N N 123 VAL HG13 H N N 124 VAL HG21 H N N 125 VAL HG22 H N N 126 VAL HG23 H N N 127 VAL HXT H N N 128 # 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 GLY N CA sing N N 1 GLY N H sing N N 2 GLY N H2 sing N N 3 GLY CA C sing N N 4 GLY CA HA2 sing N N 5 GLY CA HA3 sing N N 6 GLY C O doub N N 7 GLY C OXT sing N N 8 GLY OXT HXT sing N N 9 HOH O H1 sing N N 10 HOH O H2 sing N N 11 ILE N CA sing N N 12 ILE N H sing N N 13 ILE N H2 sing N N 14 ILE CA C sing N N 15 ILE CA CB sing N N 16 ILE CA HA sing N N 17 ILE C O doub N N 18 ILE C OXT sing N N 19 ILE CB CG1 sing N N 20 ILE CB CG2 sing N N 21 ILE CB HB sing N N 22 ILE CG1 CD1 sing N N 23 ILE CG1 HG12 sing N N 24 ILE CG1 HG13 sing N N 25 ILE CG2 HG21 sing N N 26 ILE CG2 HG22 sing N N 27 ILE CG2 HG23 sing N N 28 ILE CD1 HD11 sing N N 29 ILE CD1 HD12 sing N N 30 ILE CD1 HD13 sing N N 31 ILE OXT HXT sing N N 32 LYS N CA sing N N 33 LYS N H sing N N 34 LYS N H2 sing N N 35 LYS CA C sing N N 36 LYS CA CB sing N N 37 LYS CA HA sing N N 38 LYS C O doub N N 39 LYS C OXT sing N N 40 LYS CB CG sing N N 41 LYS CB HB2 sing N N 42 LYS CB HB3 sing N N 43 LYS CG CD sing N N 44 LYS CG HG2 sing N N 45 LYS CG HG3 sing N N 46 LYS CD CE sing N N 47 LYS CD HD2 sing N N 48 LYS CD HD3 sing N N 49 LYS CE NZ sing N N 50 LYS CE HE2 sing N N 51 LYS CE HE3 sing N N 52 LYS NZ HZ1 sing N N 53 LYS NZ HZ2 sing N N 54 LYS NZ HZ3 sing N N 55 LYS OXT HXT sing N N 56 SER N CA sing N N 57 SER N H sing N N 58 SER N H2 sing N N 59 SER CA C sing N N 60 SER CA CB sing N N 61 SER CA HA sing N N 62 SER C O doub N N 63 SER C OXT sing N N 64 SER CB OG sing N N 65 SER CB HB2 sing N N 66 SER CB HB3 sing N N 67 SER OG HG sing N N 68 SER OXT HXT sing N N 69 TFA C1 C2 sing N N 70 TFA C1 O doub N N 71 TFA C1 OXT sing N N 72 TFA C2 F1 sing N N 73 TFA C2 F2 sing N N 74 TFA C2 F3 sing N N 75 TFA OXT HXT sing N N 76 TRP N CA sing N N 77 TRP N H sing N N 78 TRP N H2 sing N N 79 TRP CA C sing N N 80 TRP CA CB sing N N 81 TRP CA HA sing N N 82 TRP C O doub N N 83 TRP C OXT sing N N 84 TRP CB CG sing N N 85 TRP CB HB2 sing N N 86 TRP CB HB3 sing N N 87 TRP CG CD1 doub Y N 88 TRP CG CD2 sing Y N 89 TRP CD1 NE1 sing Y N 90 TRP CD1 HD1 sing N N 91 TRP CD2 CE2 doub Y N 92 TRP CD2 CE3 sing Y N 93 TRP NE1 CE2 sing Y N 94 TRP NE1 HE1 sing N N 95 TRP CE2 CZ2 sing Y N 96 TRP CE3 CZ3 doub Y N 97 TRP CE3 HE3 sing N N 98 TRP CZ2 CH2 doub Y N 99 TRP CZ2 HZ2 sing N N 100 TRP CZ3 CH2 sing Y N 101 TRP CZ3 HZ3 sing N N 102 TRP CH2 HH2 sing N N 103 TRP OXT HXT sing N N 104 VAL N CA sing N N 105 VAL N H sing N N 106 VAL N H2 sing N N 107 VAL CA C sing N N 108 VAL CA CB sing N N 109 VAL CA HA sing N N 110 VAL C O doub N N 111 VAL C OXT sing N N 112 VAL CB CG1 sing N N 113 VAL CB CG2 sing N N 114 VAL CB HB sing N N 115 VAL CG1 HG11 sing N N 116 VAL CG1 HG12 sing N N 117 VAL CG1 HG13 sing N N 118 VAL CG2 HG21 sing N N 119 VAL CG2 HG22 sing N N 120 VAL CG2 HG23 sing N N 121 VAL OXT HXT sing N N 122 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'National Institutes of Health/National Institute on Aging (NIH/NIA)' 'United States' AG054022 1 'Howard Hughes Medical Institute (HHMI)' 'United States' ? 2 # _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 'two antiparallel beta strands' # _atom_sites.entry_id 5WMJ _atom_sites.fract_transf_matrix[1][1] 0.105064 _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] 0.049305 _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] 0.022599 _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 F N O # loop_