data_6FGR # _entry.id 6FGR # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 6FGR pdb_00006fgr 10.2210/pdb6fgr/pdb WWPDB D_1200008296 ? ? # 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 2018-08-08 2 'Structure model' 1 1 2018-09-12 3 'Structure model' 1 2 2019-12-25 4 'Structure model' 1 3 2022-03-30 5 'Structure model' 1 4 2024-05-01 # _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 4 'Structure model' 'Author supporting evidence' 5 4 'Structure model' 'Database references' 6 5 'Structure model' 'Data collection' 7 5 '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' reflns_shell 4 4 'Structure model' database_2 5 4 'Structure model' pdbx_audit_support 6 5 'Structure model' chem_comp_atom 7 5 'Structure model' chem_comp_bond 8 5 '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 2 'Structure model' '_citation.pdbx_database_id_DOI' 5 2 'Structure model' '_citation.pdbx_database_id_PubMed' 6 2 'Structure model' '_citation.title' 7 2 'Structure model' '_citation_author.identifier_ORCID' 8 3 'Structure model' '_reflns_shell.percent_possible_all' 9 4 'Structure model' '_database_2.pdbx_DOI' 10 4 'Structure model' '_database_2.pdbx_database_accession' 11 4 'Structure model' '_pdbx_audit_support.funding_organization' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 6FGR _pdbx_database_status.recvd_initial_deposition_date 2018-01-11 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details 'IIKVIK from PSMalpha1' _pdbx_database_related.db_id 6FG4 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Landau, M.' 1 0000-0002-1743-3430 'Colletier, J.-P.' 2 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nat Commun' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2041-1723 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 9 _citation.language ? _citation.page_first 3512 _citation.page_last 3512 _citation.title 'Extreme amyloid polymorphism in Staphylococcus aureus virulent PSM alpha peptides.' _citation.year 2018 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41467-018-05490-0 _citation.pdbx_database_id_PubMed 30158633 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Salinas, N.' 1 0000-0002-3511-2243 primary 'Colletier, J.P.' 2 ? primary 'Moshe, A.' 3 ? primary 'Landau, M.' 4 0000-0002-1743-3430 # 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 'Psm alpha-4' 729.006 2 ? ? 'Amyloid spine segment IIKIIK from PSMalpha4 (residues 7-12) secreted by S. aureus' ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 1 ? ? ? ? 3 non-polymer syn 'SULFATE ION' 96.063 2 ? ? ? ? 4 water nat water 18.015 3 ? ? ? ? # _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 IIKIIK _entity_poly.pdbx_seq_one_letter_code_can IIKIIK _entity_poly.pdbx_strand_id B,A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 'SULFATE ION' SO4 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 ILE n 1 3 LYS n 1 4 ILE n 1 5 ILE n 1 6 LYS 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 'Staphylococcus aureus' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 1280 _pdbx_entity_src_syn.details 'IIKIIK from PSMalpha4, synthesized' # 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 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 # 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 ILE 1 1 1 ILE ILE B . n A 1 2 ILE 2 2 2 ILE ILE B . n A 1 3 LYS 3 3 3 LYS LYS B . n A 1 4 ILE 4 4 4 ILE ILE B . n A 1 5 ILE 5 5 5 ILE ILE B . n A 1 6 LYS 6 6 6 LYS LYS B . n B 1 1 ILE 1 1 1 ILE ILE A . n B 1 2 ILE 2 2 2 ILE ILE A . n B 1 3 LYS 3 3 3 LYS LYS A . n B 1 4 ILE 4 4 4 ILE ILE A . n B 1 5 ILE 5 5 5 ILE ILE A . n B 1 6 LYS 6 6 6 LYS LYS 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 C 2 EDO 1 101 2 EDO EDO B . D 3 SO4 1 102 1 SO4 SO4 B . E 3 SO4 1 103 2 SO4 SO4 B . F 4 HOH 1 201 5 HOH HOH B . G 4 HOH 1 101 3 HOH HOH A . G 4 HOH 2 102 4 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 reduction' ? ? 'Wolfgang Kabsch' Wolfgang.Kabsch@mpimf-heidelberg.mpg.de ? ? ? ? ? http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ ? XDS ? ? package . 2 ? 'data scaling' ? ? 'Wolfgang Kabsch' ? ? ? ? ? ? http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html ? XSCALE ? ? package . 3 ? phasing ? ? 'Randy J. Read' cimr-phaser@lists.cam.ac.uk ? ? ? ? ? http://www-structmed.cimr.cam.ac.uk/phaser/ ? PHASER ? ? program . 4 ? 'data extraction' ? ? PDB deposit@deposit.rcsb.org 'Sep. 1, 2017' ? ? ? C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ? PDB_EXTRACT ? ? package 3.24 5 # _cell.length_a 4.830 _cell.length_b 22.380 _cell.length_c 23.060 _cell.angle_alpha 107.000 _cell.angle_beta 90.010 _cell.angle_gamma 96.200 _cell.entry_id 6FGR _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 1' _symmetry.entry_id 6FGR _symmetry.Int_Tables_number 1 _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 6FGR _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 1.62 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 24.28 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.id 1 _exptl_crystal.preparation ? _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _exptl_crystal.colour_lustre ? _exptl_crystal.colour_modifier ? _exptl_crystal.colour_primary ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_esd ? _exptl_crystal.density_meas_gt ? _exptl_crystal.density_meas_lt ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_meas_temp_esd ? _exptl_crystal.density_meas_temp_gt ? _exptl_crystal.density_meas_temp_lt ? _exptl_crystal.pdbx_crystal_image_url ? _exptl_crystal.pdbx_crystal_image_format ? _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? # _exptl_crystal_grow.apparatus ? _exptl_crystal_grow.atmosphere ? _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.details ? _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pressure ? _exptl_crystal_grow.pressure_esd ? _exptl_crystal_grow.seeding ? _exptl_crystal_grow.seeding_ref ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.temp_esd ? _exptl_crystal_grow.time ? _exptl_crystal_grow.pdbx_details 'Reservoir contained 0.2M Ammonium sulfate, 20% polyethylene glycol 3350' _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 PIXEL _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'DECTRIS PILATUS 2M' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2014-10-08 # _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 0.8729 _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 'ESRF BEAMLINE ID23-2' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.8729 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ID23-2 _diffrn_source.pdbx_synchrotron_site ESRF # _reflns.entry_id 6FGR _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 18.210 _reflns.d_resolution_high 1.500 _reflns.number_obs 1397 _reflns.number_all ? _reflns.percent_possible_obs 95.000 _reflns.pdbx_Rmerge_I_obs 0.206 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 7.180 _reflns.B_iso_Wilson_estimate 16.205 _reflns.pdbx_redundancy 9.890 _reflns.pdbx_Rrim_I_all 0.217 _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_CC_half 0.994 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_number_measured_all 13816 _reflns.pdbx_scaling_rejects 1 _reflns.pdbx_chi_squared 0.835 _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 1.500 1.560 770 ? 158 ? 0.622 2.390 ? ? 4.873 ? ? 177 ? ? ? ? ? 89.300 0.694 ? 0.744 1 2 1.560 1.620 716 ? 109 ? 0.447 3.440 ? ? 6.569 ? ? 147 ? ? ? ? ? 74.100 0.484 ? 0.920 1 3 1.620 1.690 1276 ? 133 ? 0.547 3.720 ? ? 9.594 ? ? 134 ? ? ? ? ? 99.300 0.577 ? 0.857 1 4 1.690 1.780 1234 ? 118 ? 0.521 4.260 ? ? 10.458 ? ? 118 ? ? ? ? ? 100.000 0.550 ? 0.879 1 5 1.780 1.870 1289 ? 120 ? 0.380 4.800 ? ? 10.742 ? ? 121 ? ? ? ? ? 99.200 0.399 ? 0.971 1 6 1.870 1.990 1428 ? 125 ? 0.251 7.970 ? ? 11.424 ? ? 126 ? ? ? ? ? 99.200 0.262 ? 0.990 1 7 1.990 2.120 1527 ? 130 ? 0.260 8.290 ? ? 11.746 ? ? 131 ? ? ? ? ? 99.200 0.272 ? 0.977 1 8 2.120 2.290 1464 ? 122 ? 0.223 9.970 ? ? 12.000 ? ? 118 ? ? ? ? ? 100 0.233 ? 0.984 1 9 2.290 2.510 847 ? 89 ? 0.214 8.640 ? ? 9.517 ? ? 101 ? ? ? ? ? 88.100 0.226 ? 0.992 1 10 2.510 2.810 767 ? 73 ? 0.179 9.700 ? ? 10.507 ? ? 75 ? ? ? ? ? 97.300 0.188 ? 0.996 1 11 2.810 3.240 735 ? 69 ? 0.182 10.140 ? ? 10.652 ? ? 69 ? ? ? ? ? 100.000 0.190 ? 0.996 1 12 3.240 3.970 842 ? 74 ? 0.150 14.200 ? ? 11.378 ? ? 74 ? ? ? ? ? 100.000 0.156 ? 0.994 1 13 3.970 5.620 680 ? 57 ? 0.126 16.510 ? ? 11.930 ? ? 58 ? ? ? ? ? 98.300 0.132 ? 0.989 1 14 5.620 18.210 241 ? 20 ? 0.096 12.380 ? ? 12.050 ? ? 22 ? ? ? ? ? 90.900 0.100 ? 1.000 # _refine.entry_id 6FGR _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 1.5000 _refine.ls_d_res_low 18.2100 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 95.1000 _refine.ls_number_reflns_obs 1257 _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 0.1869 _refine.ls_R_factor_R_work 0.1828 _refine.ls_wR_factor_R_work 0.1868 _refine.ls_R_factor_R_free 0.2215 _refine.ls_wR_factor_R_free 0.2222 _refine.ls_percent_reflns_R_free 10.0000 _refine.ls_number_reflns_R_free 140 _refine.ls_number_reflns_R_work ? _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 9.1280 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 0.0000 _refine.aniso_B[2][2] -0.3000 _refine.aniso_B[3][3] 0.3300 _refine.aniso_B[1][2] -0.0500 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] -0.1300 _refine.correlation_coeff_Fo_to_Fc 0.9590 _refine.correlation_coeff_Fo_to_Fc_free 0.9440 _refine.overall_SU_R_Cruickshank_DPI 0.3052 _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 0.1113 _refine.pdbx_overall_ESU_R 0.3050 _refine.pdbx_overall_ESU_R_Free 0.1110 _refine.overall_SU_ML 0.0710 _refine.overall_SU_B 4.3470 _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 'ideal beta-strand of poly-ala' _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 0.8212 _refine.B_iso_max 61.860 _refine.B_iso_min 1.710 _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 1.5000 _refine_hist.d_res_low 18.2100 _refine_hist.pdbx_number_atoms_ligand 22 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 127 _refine_hist.pdbx_number_residues_total 12 _refine_hist.pdbx_B_iso_mean_ligand 30.37 _refine_hist.pdbx_B_iso_mean_solvent 26.93 _refine_hist.pdbx_number_atoms_protein 102 _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 117 0.010 0.020 ? ? 'X-RAY DIFFRACTION' r_bond_other_d 159 0.019 0.020 ? ? 'X-RAY DIFFRACTION' r_angle_refined_deg 148 1.903 2.226 ? ? 'X-RAY DIFFRACTION' r_angle_other_deg 365 0.958 3.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_1_deg 10 7.356 5.000 ? ? 'X-RAY DIFFRACTION' r_dihedral_angle_3_deg 32 14.769 15.000 ? ? 'X-RAY DIFFRACTION' r_chiral_restr 22 0.120 0.200 ? ? 'X-RAY DIFFRACTION' r_gen_planes_refined 78 0.006 0.020 ? ? 'X-RAY DIFFRACTION' r_gen_planes_other 10 0.001 0.020 ? ? 'X-RAY DIFFRACTION' r_rigid_bond_restr 276 8.146 3.000 ? ? 'X-RAY DIFFRACTION' r_sphericity_free 1 8.676 5.000 ? ? 'X-RAY DIFFRACTION' r_sphericity_bonded 285 2.709 5.000 ? ? # _refine_ls_shell.d_res_high 1.5020 _refine_ls_shell.d_res_low 1.5400 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 93.8600 _refine_ls_shell.number_reflns_R_work 96 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.2640 _refine_ls_shell.R_factor_R_free 0.2610 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 11 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.number_reflns_all 107 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _struct.entry_id 6FGR _struct.title 'Crystal Structure of the Amyloid-like IIKIIK Segment from the S. aureus Biofilm-associated PSMalpha4' _struct.pdbx_model_details 'Phenol Soluble Modulin' _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6FGR _struct_keywords.text 'steric-zipper, cross-beta, bacterial amyloid fibril, S. aureus, PSM, 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 ? F N N 4 ? G N N 4 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code H9BRQ8_STAAU _struct_ref.pdbx_db_accession H9BRQ8 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code IIKIIK _struct_ref.pdbx_align_begin 7 # 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 6FGR B 1 ? 6 ? H9BRQ8 7 ? 12 ? 1 6 2 1 6FGR A 1 ? 6 ? H9BRQ8 7 ? 12 ? 1 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,B,C,D,E,F,G 1 2 A,B,C,D,E,F,G 1 3 A,B,C,D,E,F,G 1 4 A,B,C,D,E,F,G 1 5 A,B,C,D,E,F,G 1 6 A,B,C,D,E,F,G 1 7 A,B,C,D,E,F,G 1 8 A,B,C,D,E,F,G 1 9 A,B,C,D,E,F,G # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support microscopy _pdbx_struct_assembly_auth_evidence.details 'Fibrils were visualized by electron microscopy' # 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_155 x-4,y,z 1.0000000000 0.0000000000 0.0000000000 -19.3200000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_255 x-3,y,z 1.0000000000 0.0000000000 0.0000000000 -14.4900000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_355 x-2,y,z 1.0000000000 0.0000000000 0.0000000000 -9.6600000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 1_455 x-1,y,z 1.0000000000 0.0000000000 0.0000000000 -4.8300000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 1_655 x+1,y,z 1.0000000000 0.0000000000 0.0000000000 4.8300000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 7 'crystal symmetry operation' 1_755 x+2,y,z 1.0000000000 0.0000000000 0.0000000000 9.6600000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 8 'crystal symmetry operation' 1_855 x+3,y,z 1.0000000000 0.0000000000 0.0000000000 14.4900000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9 'crystal symmetry operation' 1_955 x+4,y,z 1.0000000000 0.0000000000 0.0000000000 19.3200000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B EDO 101 ? 6 'binding site for residue EDO B 101' AC2 Software B SO4 102 ? 8 'binding site for residue SO4 B 102' AC3 Software B SO4 103 ? 7 'binding site for residue SO4 B 103' # 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 6 LYS B 3 ? LYS A 3 . ? 1_665 ? 2 AC1 6 LYS B 3 ? LYS A 3 . ? 1_565 ? 3 AC1 6 LYS B 6 ? LYS A 6 . ? 1_555 ? 4 AC1 6 LYS A 3 ? LYS B 3 . ? 1_655 ? 5 AC1 6 LYS A 3 ? LYS B 3 . ? 1_555 ? 6 AC1 6 LYS A 6 ? LYS B 6 . ? 1_665 ? 7 AC2 8 ILE B 1 ? ILE A 1 . ? 1_554 ? 8 AC2 8 ILE B 1 ? ILE A 1 . ? 1_654 ? 9 AC2 8 LYS B 6 ? LYS A 6 . ? 1_444 ? 10 AC2 8 LYS B 6 ? LYS A 6 . ? 1_544 ? 11 AC2 8 LYS A 6 ? LYS B 6 . ? 1_655 ? 12 AC2 8 LYS A 6 ? LYS B 6 . ? 1_555 ? 13 AC2 8 SO4 E . ? SO4 B 103 . ? 1_555 ? 14 AC2 8 HOH F . ? HOH B 201 . ? 1_555 ? 15 AC3 7 LYS B 6 ? LYS A 6 . ? 1_444 ? 16 AC3 7 LYS B 6 ? LYS A 6 . ? 1_544 ? 17 AC3 7 ILE A 1 ? ILE B 1 . ? 1_645 ? 18 AC3 7 ILE A 1 ? ILE B 1 . ? 1_545 ? 19 AC3 7 LYS A 6 ? LYS B 6 . ? 1_655 ? 20 AC3 7 LYS A 6 ? LYS B 6 . ? 1_555 ? 21 AC3 7 SO4 D . ? SO4 B 102 . ? 1_555 ? # _pdbx_phasing_MR.entry_id 6FGR _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor ? _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation ? _pdbx_phasing_MR.d_res_low_rotation ? _pdbx_phasing_MR.d_res_high_translation ? _pdbx_phasing_MR.d_res_low_translation ? _pdbx_phasing_MR.packing 0.000 _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # 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 EDO C1 C N N 1 EDO O1 O N N 2 EDO C2 C N N 3 EDO O2 O N N 4 EDO H11 H N N 5 EDO H12 H N N 6 EDO HO1 H N N 7 EDO H21 H N N 8 EDO H22 H N N 9 EDO HO2 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 SO4 S S N N 61 SO4 O1 O N N 62 SO4 O2 O N N 63 SO4 O3 O N N 64 SO4 O4 O N N 65 # 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 EDO C1 O1 sing N N 1 EDO C1 C2 sing N N 2 EDO C1 H11 sing N N 3 EDO C1 H12 sing N N 4 EDO O1 HO1 sing N N 5 EDO C2 O2 sing N N 6 EDO C2 H21 sing N N 7 EDO C2 H22 sing N N 8 EDO O2 HO2 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 SO4 S O1 doub N N 57 SO4 S O2 doub N N 58 SO4 S O3 sing N N 59 SO4 S O4 sing N N 60 # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Israel Science Foundation' Israel 560/16 1 'Deutsch-IsraelischeProjektkooperation (DIP)' Israel 3655/1-1 2 'I-CORE Program of the Planning and Budgeting Committee and The Israel Science Foundation' Israel 1775/12 3 'United States - Israel Binational Science Foundation (BSF)' Israel 2013254 4 # _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 'ideal beta-strand of poly-ala' # _atom_sites.entry_id 6FGR _atom_sites.fract_transf_matrix[1][1] 0.207039 _atom_sites.fract_transf_matrix[1][2] 0.022499 _atom_sites.fract_transf_matrix[1][3] 0.006967 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.044946 _atom_sites.fract_transf_matrix[2][3] 0.013835 _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] 0.045373 _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 S # loop_