data_6PQA # _entry.id 6PQA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 6PQA pdb_00006pqa 10.2210/pdb6pqa/pdb WWPDB D_1000242876 ? ? # 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 2020-04-15 2 'Structure model' 1 1 2020-04-29 3 'Structure model' 1 2 2020-05-27 4 'Structure model' 1 3 2024-03-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' # 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' chem_comp_atom 5 4 'Structure model' chem_comp_bond 6 4 'Structure model' database_2 # 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.pdbx_database_id_PubMed' 2 2 'Structure model' '_citation.title' 3 2 'Structure model' '_citation_author.name' 4 3 'Structure model' '_citation.journal_volume' 5 3 'Structure model' '_citation.page_first' 6 3 'Structure model' '_citation.page_last' 7 4 'Structure model' '_database_2.pdbx_DOI' 8 4 '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 6PQA _pdbx_database_status.recvd_initial_deposition_date 2019-07-08 _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 ? # _pdbx_database_related.db_name PDB _pdbx_database_related.details 'AGAAAA segment 113-118 from human prion' _pdbx_database_related.db_id 6PQ5 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Apostol, M.I.' 1 ? 'Sawaya, M.R.' 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 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 27 _citation.language ? _citation.page_first 417 _citation.page_last 423 _citation.title 'Cryo-EM structure of a human prion fibril with a hydrophobic, protease-resistant core.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s41594-020-0403-y _citation.pdbx_database_id_PubMed 32284600 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Glynn, C.' 1 ? primary 'Sawaya, M.R.' 2 ? primary 'Ge, P.' 3 ? primary 'Gallagher-Jones, M.' 4 ? primary 'Short, C.W.' 5 ? primary 'Bowman, R.' 6 ? primary 'Apostol, M.' 7 ? primary 'Zhou, Z.H.' 8 ? primary 'Eisenberg, D.S.' 9 ? primary 'Rodriguez, J.A.' 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 'Major prion protein' 458.510 1 ? ? 'UNP residues 119-124' ? 2 water nat water 18.015 3 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'PrP, ASCR, PrP27-30, PrP33-35C' # _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 GAVVGG _entity_poly.pdbx_seq_one_letter_code_can GAVVGG _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 ALA n 1 3 VAL n 1 4 VAL n 1 5 GLY n 1 6 GLY 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 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 GLY 1 1 1 GLY GLY A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 VAL 4 4 4 VAL VAL A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 GLY 6 6 6 GLY GLY 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 1 101 2 HOH HOH A . B 2 HOH 2 102 1 HOH HOH A . B 2 HOH 3 103 3 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 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DENZO ? ? ? . 1 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALEPACK ? ? ? 1.97.8 2 ? phasing ? ? ? ? ? ? ? ? ? ? ? PHASER ? ? ? 1.3.2 3 ? refinement ? ? ? ? ? ? ? ? ? ? ? REFMAC ? ? ? 5.4.0061 4 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.25 5 # _cell.angle_alpha 90.000 _cell.angle_alpha_esd ? _cell.angle_beta 92.380 _cell.angle_beta_esd ? _cell.angle_gamma 90.000 _cell.angle_gamma_esd ? _cell.entry_id 6PQA _cell.details ? _cell.formula_units_Z ? _cell.length_a 4.786 _cell.length_a_esd ? _cell.length_b 12.810 _cell.length_b_esd ? _cell.length_c 20.771 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 2 _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PQA _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 6PQA _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 1.39 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 11.35 _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 7.0 _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 '10 mg/mL peptide in 2.4 M sodium malonate, pH 7.0' _exptl_crystal_grow.pdbx_pH_range 6.8-7.2 # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? _diffrn.pdbx_serial_crystal_experiment N # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MAR CCD 165 mm' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2006-05-13 _diffrn_detector.pdbx_frequency ? # _diffrn_radiation.collimation ? _diffrn_radiation.diffrn_id 1 _diffrn_radiation.filter_edge ? _diffrn_radiation.inhomogeneity ? _diffrn_radiation.monochromator 'Si(111)' _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 0.9465 _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 ID13' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.9465 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline ID13 _diffrn_source.pdbx_synchrotron_site ESRF # _reflns.B_iso_Wilson_estimate ? _reflns.entry_id 6PQA _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.450 _reflns.d_resolution_low 30.000 _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 455 _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 93.600 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 5.400 _reflns.pdbx_Rmerge_I_obs 0.145 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value 0.15 _reflns.pdbx_netI_over_av_sigmaI ? _reflns.pdbx_netI_over_sigmaI 31.400 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.052 _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 ? _reflns.pdbx_Rpim_I_all ? _reflns.pdbx_d_opt ? _reflns.pdbx_number_measured_all ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_CC_half ? _reflns.pdbx_R_split ? # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.meanI_over_sigI_all _reflns_shell.meanI_over_sigI_obs _reflns_shell.number_measured_all _reflns_shell.number_measured_obs _reflns_shell.number_possible _reflns_shell.number_unique_all _reflns_shell.number_unique_obs _reflns_shell.percent_possible_all _reflns_shell.percent_possible_obs _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_gt _reflns_shell.meanI_over_uI_all _reflns_shell.meanI_over_uI_gt _reflns_shell.number_measured_gt _reflns_shell.number_unique_gt _reflns_shell.percent_possible_gt _reflns_shell.Rmerge_F_gt _reflns_shell.Rmerge_I_gt _reflns_shell.pdbx_redundancy _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_netI_over_sigmaI_all _reflns_shell.pdbx_netI_over_sigmaI_obs _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_rejects _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_CC_half _reflns_shell.pdbx_R_split 1.450 1.500 ? ? ? ? ? ? 41 93.200 ? ? ? ? 0.311 ? ? ? ? ? ? ? ? 2.800 0.31 1.006 ? ? ? ? ? 1 1 ? ? 1.500 1.560 ? ? ? ? ? ? 48 84.200 ? ? ? ? 0.274 ? ? ? ? ? ? ? ? 3.700 ? 1.099 ? ? ? ? ? 2 1 ? ? 1.560 1.630 ? ? ? ? ? ? 41 80.400 ? ? ? ? 0.187 ? ? ? ? ? ? ? ? 4.500 ? 0.962 ? ? ? ? ? 3 1 ? ? 1.630 1.720 ? ? ? ? ? ? 36 100.000 ? ? ? ? 0.218 ? ? ? ? ? ? ? ? 6.100 ? 1.145 ? ? ? ? ? 4 1 ? ? 1.720 1.830 ? ? ? ? ? ? 46 100.000 ? ? ? ? 0.242 ? ? ? ? ? ? ? ? 6.500 ? 1.124 ? ? ? ? ? 5 1 ? ? 1.830 1.970 ? ? ? ? ? ? 48 100.000 ? ? ? ? 0.137 ? ? ? ? ? ? ? ? 6.100 ? 1.291 ? ? ? ? ? 6 1 ? ? 1.970 2.170 ? ? ? ? ? ? 51 100.000 ? ? ? ? 0.143 ? ? ? ? ? ? ? ? 6.200 ? 0.888 ? ? ? ? ? 7 1 ? ? 2.170 2.480 ? ? ? ? ? ? 50 94.300 ? ? ? ? 0.152 ? ? ? ? ? ? ? ? 5.900 ? 1.003 ? ? ? ? ? 8 1 ? ? 2.480 3.120 ? ? ? ? ? ? 44 100.000 ? ? ? ? 0.132 ? ? ? ? ? ? ? ? 6.400 ? 0.984 ? ? ? ? ? 9 1 ? ? 3.120 30.000 ? ? ? ? ? ? 50 89.300 ? ? ? ? 0.095 ? ? ? ? ? ? ? ? 5.400 ? 0.998 ? ? ? ? ? 10 1 ? ? # _refine.aniso_B[1][1] -0.3000 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] -0.2800 _refine.aniso_B[2][2] 0.8800 _refine.aniso_B[2][3] 0.0000 _refine.aniso_B[3][3] -0.6000 _refine.B_iso_max 33.980 _refine.B_iso_mean 4.4250 _refine.B_iso_min 0.880 _refine.correlation_coeff_Fo_to_Fc 0.9480 _refine.correlation_coeff_Fo_to_Fc_free 0.8780 _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _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 6PQA _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 1.4600 _refine.ls_d_res_low 20.7500 _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 389 _refine.ls_number_reflns_R_free 46 _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 92.7500 _refine.ls_percent_reflns_R_free 10.6000 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1867 _refine.ls_R_factor_R_free 0.2379 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1802 _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 ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _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 0.000 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.1050 _refine.pdbx_overall_ESU_R_Free 0.1110 _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _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 ? _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 1.0990 _refine.overall_SU_ML 0.0440 _refine.overall_SU_R_Cruickshank_DPI 0.1047 _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id final _refine_hist.details ? _refine_hist.d_res_high 1.4600 _refine_hist.d_res_low 20.7500 _refine_hist.number_atoms_solvent 3 _refine_hist.number_atoms_total 35 _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 6 _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent 31.46 _refine_hist.pdbx_number_atoms_protein 32 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _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' ? 0.007 0.022 31 ? r_bond_refined_d ? ? 'X-RAY DIFFRACTION' ? 0.001 0.020 16 ? r_bond_other_d ? ? 'X-RAY DIFFRACTION' ? 1.081 2.039 41 ? r_angle_refined_deg ? ? 'X-RAY DIFFRACTION' ? 0.554 3.000 40 ? r_angle_other_deg ? ? 'X-RAY DIFFRACTION' ? 7.501 5.000 5 ? r_dihedral_angle_1_deg ? ? 'X-RAY DIFFRACTION' ? 5.267 15.000 2 ? r_dihedral_angle_3_deg ? ? 'X-RAY DIFFRACTION' ? 0.073 0.200 5 ? r_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.003 0.020 39 ? r_gen_planes_refined ? ? 'X-RAY DIFFRACTION' ? 0.000 0.020 5 ? r_gen_planes_other ? ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.d_res_high 1.4600 _refine_ls_shell.d_res_low 1.6270 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 10 _refine_ls_shell.number_reflns_R_work 108 _refine_ls_shell.percent_reflns_obs 83.6900 _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 0.2930 _refine_ls_shell.R_factor_R_free_error 0.0000 _refine_ls_shell.R_factor_R_work 0.2040 _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_total_number_of_bins_used ? _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? # _struct.entry_id 6PQA _struct.title 'GAVVGG segment 119-124 from human prion' _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 6PQA _struct_keywords.text 'amyloid-like protofibril, 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 PRIO_HUMAN _struct_ref.pdbx_db_accession P04156 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code GAVVGG _struct_ref.pdbx_align_begin 119 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6PQA _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 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P04156 _struct_ref_seq.db_align_beg 119 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 124 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 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 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 # _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 4.7860000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_755 x+2,y,z 1.0000000000 0.0000000000 0.0000000000 9.5720000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_855 x+3,y,z 1.0000000000 0.0000000000 0.0000000000 14.3580000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 5 'crystal symmetry operation' 2_554 -x,y+1/2,-z-1 -1.0000000000 0.0000000000 0.0000000000 0.8625550639 0.0000000000 1.0000000000 0.0000000000 6.4050000000 0.0000000000 0.0000000000 -1.0000000000 -20.7530826568 6 'crystal symmetry operation' 2_654 -x+1,y+1/2,-z-1 -1.0000000000 0.0000000000 0.0000000000 5.6485550639 0.0000000000 1.0000000000 0.0000000000 6.4050000000 0.0000000000 0.0000000000 -1.0000000000 -20.7530826568 7 'crystal symmetry operation' 2_754 -x+2,y+1/2,-z-1 -1.0000000000 0.0000000000 0.0000000000 10.4345550639 0.0000000000 1.0000000000 0.0000000000 6.4050000000 0.0000000000 0.0000000000 -1.0000000000 -20.7530826568 8 'crystal symmetry operation' 2_854 -x+3,y+1/2,-z-1 -1.0000000000 0.0000000000 0.0000000000 15.2205550639 0.0000000000 1.0000000000 0.0000000000 6.4050000000 0.0000000000 0.0000000000 -1.0000000000 -20.7530826568 # _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 ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 GLY N N N N 14 GLY CA C N N 15 GLY C C N N 16 GLY O O N N 17 GLY OXT O N N 18 GLY H H N N 19 GLY H2 H N N 20 GLY HA2 H N N 21 GLY HA3 H N N 22 GLY HXT H N N 23 HOH O O N N 24 HOH H1 H N N 25 HOH H2 H N N 26 VAL N N N N 27 VAL CA C N S 28 VAL C C N N 29 VAL O O N N 30 VAL CB C N N 31 VAL CG1 C N N 32 VAL CG2 C N N 33 VAL OXT O N N 34 VAL H H N N 35 VAL H2 H N N 36 VAL HA H N N 37 VAL HB H N N 38 VAL HG11 H N N 39 VAL HG12 H N N 40 VAL HG13 H N N 41 VAL HG21 H N N 42 VAL HG22 H N N 43 VAL HG23 H N N 44 VAL HXT H N N 45 # 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 ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 GLY N CA sing N N 13 GLY N H sing N N 14 GLY N H2 sing N N 15 GLY CA C sing N N 16 GLY CA HA2 sing N N 17 GLY CA HA3 sing N N 18 GLY C O doub N N 19 GLY C OXT sing N N 20 GLY OXT HXT sing N N 21 HOH O H1 sing N N 22 HOH O H2 sing N N 23 VAL N CA sing N N 24 VAL N H sing N N 25 VAL N H2 sing N N 26 VAL CA C sing N N 27 VAL CA CB sing N N 28 VAL CA HA sing N N 29 VAL C O doub N N 30 VAL C OXT sing N N 31 VAL CB CG1 sing N N 32 VAL CB CG2 sing N N 33 VAL CB HB sing N N 34 VAL CG1 HG11 sing N N 35 VAL CG1 HG12 sing N N 36 VAL CG1 HG13 sing N N 37 VAL CG2 HG21 sing N N 38 VAL CG2 HG22 sing N N 39 VAL CG2 HG23 sing N N 40 VAL OXT HXT sing N N 41 # 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' 'R01 AG029430' 1 'National Institutes of Health/National Institute on Aging (NIH/NIA)' 'United States' 'R01 AG029430-05' 2 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' 'T32 GM007185' 3 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' 'United States' GM007185 4 # _atom_sites.entry_id 6PQA _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 0.208943 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.008673 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.078064 _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] 0.048186 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O # loop_