data_4UBY # _entry.id 4UBY # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.383 _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 4UBY pdb_00004uby 10.2210/pdb4uby/pdb WWPDB D_1000203139 ? ? # 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 2015-05-27 2 'Structure model' 1 1 2015-06-03 3 'Structure model' 1 2 2015-07-01 4 'Structure model' 1 3 2017-11-22 5 'Structure model' 1 4 2023-12-27 # _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' 'Derived calculations' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Database references' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' 6 4 'Structure model' 'Source and taxonomy' 7 5 'Structure model' 'Data collection' 8 5 '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 4 'Structure model' citation 2 4 'Structure model' pdbx_entity_src_syn 3 4 'Structure model' pdbx_struct_assembly 4 4 'Structure model' pdbx_struct_assembly_gen 5 4 'Structure model' pdbx_struct_oper_list 6 4 'Structure model' software 7 5 'Structure model' chem_comp_atom 8 5 'Structure model' chem_comp_bond 9 5 '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 4 'Structure model' '_citation.journal_id_CSD' 2 4 'Structure model' '_pdbx_entity_src_syn.pdbx_alt_source_flag' 3 4 'Structure model' '_pdbx_struct_assembly.oligomeric_details' 4 4 'Structure model' '_pdbx_struct_assembly_gen.asym_id_list' 5 4 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 6 5 'Structure model' '_database_2.pdbx_DOI' 7 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 4UBY _pdbx_database_status.recvd_initial_deposition_date 2014-08-13 _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_ _pdbx_database_related.content_type _pdbx_database_related.db_id _pdbx_database_related.db_name _pdbx_database_related.details unspecified 4UBZ PDB . unspecified 4W5L PDB . unspecified 4W5M PDB . unspecified 4W5P PDB . unspecified 4W5Y PDB . unspecified 4W67 PDB . unspecified 4W71 PDB . unspecified 4WBU PDB . unspecified 4WBV PDB . unspecified 4TUT PDB . # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yu, L.' 1 'Lee, S.-J.' 2 'Yee, V.' 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 Biochemistry _citation.journal_id_ASTM BICHAW _citation.journal_id_CSD 0033 _citation.journal_id_ISSN 0006-2960 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 54 _citation.language ? _citation.page_first 3640 _citation.page_last 3648 _citation.title 'Crystal Structures of Polymorphic Prion Protein beta 1 Peptides Reveal Variable Steric Zipper Conformations.' _citation.year 2015 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biochem.5b00425 _citation.pdbx_database_id_PubMed 25978088 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yu, L.' 1 ? primary 'Lee, S.J.' 2 ? primary 'Yee, V.C.' 3 ? # 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 'prion peptide' 564.633 4 ? ? ? ? 2 water nat water 18.015 22 ? ? ? ? # _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 GGYVLG _entity_poly.pdbx_seq_one_letter_code_can GGYVLG _entity_poly.pdbx_strand_id A,B,C,D _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 GLY n 1 3 TYR n 1 4 VAL n 1 5 LEU 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 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 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 1 126 126 GLY GLY A . n A 1 2 GLY 2 127 127 GLY GLY A . n A 1 3 TYR 3 128 128 TYR TYR A . n A 1 4 VAL 4 129 129 VAL VAL A . n A 1 5 LEU 5 130 130 LEU LEU A . n A 1 6 GLY 6 131 131 GLY GLY A . n B 1 1 GLY 1 126 126 GLY GLY B . n B 1 2 GLY 2 127 127 GLY GLY B . n B 1 3 TYR 3 128 128 TYR TYR B . n B 1 4 VAL 4 129 129 VAL VAL B . n B 1 5 LEU 5 130 130 LEU LEU B . n B 1 6 GLY 6 131 131 GLY GLY B . n C 1 1 GLY 1 126 126 GLY GLY C . n C 1 2 GLY 2 127 127 GLY GLY C . n C 1 3 TYR 3 128 128 TYR TYR C . n C 1 4 VAL 4 129 129 VAL VAL C . n C 1 5 LEU 5 130 130 LEU LEU C . n C 1 6 GLY 6 131 131 GLY GLY C . n D 1 1 GLY 1 126 126 GLY GLY D . n D 1 2 GLY 2 127 127 GLY GLY D . n D 1 3 TYR 3 128 128 TYR TYR D . n D 1 4 VAL 4 129 129 VAL VAL D . n D 1 5 LEU 5 130 130 LEU LEU D . n D 1 6 GLY 6 131 131 GLY GLY D . 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 E 2 HOH 1 201 19 HOH HOH A . E 2 HOH 2 202 3 HOH HOH A . F 2 HOH 1 201 22 HOH HOH B . F 2 HOH 2 202 14 HOH HOH B . F 2 HOH 3 203 17 HOH HOH B . F 2 HOH 4 204 9 HOH HOH B . F 2 HOH 5 205 8 HOH HOH B . F 2 HOH 6 206 1 HOH HOH B . F 2 HOH 7 207 5 HOH HOH B . F 2 HOH 8 208 10 HOH HOH B . F 2 HOH 9 209 20 HOH HOH B . F 2 HOH 10 210 18 HOH HOH B . G 2 HOH 1 201 7 HOH HOH C . G 2 HOH 2 202 21 HOH HOH C . G 2 HOH 3 203 6 HOH HOH C . G 2 HOH 4 204 13 HOH HOH C . G 2 HOH 5 205 4 HOH HOH C . G 2 HOH 6 206 2 HOH HOH C . H 2 HOH 1 201 15 HOH HOH D . H 2 HOH 2 202 11 HOH HOH D . H 2 HOH 3 203 16 HOH HOH D . H 2 HOH 4 204 12 HOH HOH D . # 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' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 1 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.14 2 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? HKL-2000 ? ? ? . 3 ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(phenix.refine: 1.9_1692)' 4 ? phasing ? ? ? ? ? ? ? ? ? ? ? SHELX ? ? ? . 5 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DENZO ? ? ? . 6 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALEPACK ? ? ? . 7 # _cell.length_a 11.666 _cell.length_b 17.145 _cell.length_c 19.073 _cell.angle_alpha 79.760 _cell.angle_beta 86.510 _cell.angle_gamma 90.200 _cell.entry_id 4UBY _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4UBY _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 4UBY _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 1.66 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol 25.86 _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, SITTING DROP' _exptl_crystal_grow.method_ref ? _exptl_crystal_grow.pH 4.6 _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 '0.1 M sodium acetate, and 2 M ammonium sulfate' _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.ambient_environment ? _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.ambient_temp_esd ? _diffrn.crystal_id 1 _diffrn.crystal_support ? _diffrn.crystal_treatment ? _diffrn.details ? _diffrn.id 1 _diffrn.ambient_pressure ? _diffrn.ambient_pressure_esd ? _diffrn.ambient_pressure_gt ? _diffrn.ambient_pressure_lt ? _diffrn.ambient_temp_gt ? _diffrn.ambient_temp_lt ? # _diffrn_detector.details ? _diffrn_detector.detector CCD _diffrn_detector.diffrn_id 1 _diffrn_detector.type 'MARMOSAIC 300 mm CCD' _diffrn_detector.area_resol_mean ? _diffrn_detector.dtime ? _diffrn_detector.pdbx_frames_total ? _diffrn_detector.pdbx_collection_time_total ? _diffrn_detector.pdbx_collection_date 2011-10-20 # _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 0.7749 _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 23-ID-B' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.7749 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 23-ID-B _diffrn_source.pdbx_synchrotron_site APS # _reflns.B_iso_Wilson_estimate 2.670 _reflns.entry_id 4UBY _reflns.data_reduction_details ? _reflns.data_reduction_method ? _reflns.d_resolution_high 1.000 _reflns.d_resolution_low 50.000 _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 6346 _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 80.900 _reflns.R_free_details ? _reflns.Rmerge_F_all ? _reflns.Rmerge_F_obs ? _reflns.Friedel_coverage ? _reflns.number_gt ? _reflns.threshold_expression ? _reflns.pdbx_redundancy 2.800 _reflns.pdbx_Rmerge_I_obs 0.062 _reflns.pdbx_Rmerge_I_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 16.260 _reflns.pdbx_netI_over_sigmaI 24.600 _reflns.pdbx_res_netI_over_av_sigmaI_2 ? _reflns.pdbx_res_netI_over_sigmaI_2 ? _reflns.pdbx_chi_squared 1.016 _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 18020 _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 1.000 1.040 ? ? ? ? ? 455 ? 57.600 ? ? ? ? 0.101 ? ? ? ? ? ? ? ? 1.900 ? 1.268 ? ? ? ? 0 1 1 ? ? 1.040 1.080 ? ? ? ? ? 521 ? 66.200 ? ? ? ? 0.070 ? ? ? ? ? ? ? ? 2.400 ? 0.939 ? ? ? ? 0 2 1 ? ? 1.080 1.130 ? ? ? ? ? 565 ? 74.100 ? ? ? ? 0.066 ? ? ? ? ? ? ? ? 2.600 ? 1.099 ? ? ? ? 0 3 1 ? ? 1.130 1.190 ? ? ? ? ? 622 ? 78.900 ? ? ? ? 0.066 ? ? ? ? ? ? ? ? 2.800 ? 0.955 ? ? ? ? 0 4 1 ? ? 1.190 1.260 ? ? ? ? ? 665 ? 84.200 ? ? ? ? 0.075 ? ? ? ? ? ? ? ? 2.700 ? 1.074 ? ? ? ? 0 5 1 ? ? 1.260 1.360 ? ? ? ? ? 646 ? 83.100 ? ? ? ? 0.065 ? ? ? ? ? ? ? ? 2.700 ? 1.006 ? ? ? ? 0 6 1 ? ? 1.360 1.490 ? ? ? ? ? 688 ? 87.000 ? ? ? ? 0.064 ? ? ? ? ? ? ? ? 2.900 ? 0.977 ? ? ? ? 0 7 1 ? ? 1.490 1.710 ? ? ? ? ? 735 ? 91.800 ? ? ? ? 0.062 ? ? ? ? ? ? ? ? 3.200 ? 0.957 ? ? ? ? 0 8 1 ? ? 1.710 2.150 ? ? ? ? ? 744 ? 95.600 ? ? ? ? 0.060 ? ? ? ? ? ? ? ? 3.400 ? 1.024 ? ? ? ? 0 9 1 ? ? 2.150 50.000 ? ? ? ? ? 705 ? 89.900 ? ? ? ? 0.058 ? ? ? ? ? ? ? ? 3.400 ? 1.030 ? ? ? ? 0 10 1 ? ? # _refine.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _refine.B_iso_max 34.080 _refine.B_iso_mean 5.8555 _refine.B_iso_min 1.640 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details ? _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 4UBY _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 1.0000 _refine.ls_d_res_low 13.8220 _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 6341 _refine.ls_number_reflns_R_free 280 _refine.ls_number_reflns_R_work 6061 _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 80.7600 _refine.ls_percent_reflns_R_free 4.4200 _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1218 _refine.ls_R_factor_R_free 0.1577 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work 0.1201 _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.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 2.320 _refine.pdbx_ls_sigma_Fsqd ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_R_Free_selection_details 'Random selection' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _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 16.8600 _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id 1 _refine.overall_SU_B ? _refine.overall_SU_ML 0.0600 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? # _refine_hist.cycle_id final _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.d_res_high 1.0000 _refine_hist.d_res_low 13.8220 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 22 _refine_hist.number_atoms_total 182 _refine_hist.pdbx_number_residues_total 24 _refine_hist.pdbx_B_iso_mean_solvent 20.88 _refine_hist.pdbx_number_atoms_protein 160 _refine_hist.pdbx_number_atoms_nucleic_acid 0 # 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' ? 0.006 ? 174 ? f_bond_d ? ? 'X-RAY DIFFRACTION' ? 1.068 ? 231 ? f_angle_d ? ? 'X-RAY DIFFRACTION' ? 0.053 ? 20 ? f_chiral_restr ? ? 'X-RAY DIFFRACTION' ? 0.004 ? 33 ? f_plane_restr ? ? 'X-RAY DIFFRACTION' ? 9.818 ? 53 ? f_dihedral_angle_d ? ? # loop_ _refine_ls_shell.pdbx_refine_id _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.number_reflns_R_free _refine_ls_shell.number_reflns_R_work _refine_ls_shell.percent_reflns_obs _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_obs _refine_ls_shell.R_factor_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.R_factor_R_work _refine_ls_shell.redundancy_reflns_all _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.wR_factor_all _refine_ls_shell.wR_factor_obs _refine_ls_shell.wR_factor_R_free _refine_ls_shell.wR_factor_R_work _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.pdbx_phase_error 'X-RAY DIFFRACTION' 0.9996 1.2592 2818 . 126 2692 72.0000 . . . 0.1320 . 0.0990 . . . . . . 2 . 'X-RAY DIFFRACTION' 1.2592 13.8229 3523 . 154 3369 90.0000 . . . 0.1708 . 0.1307 . . . . . . 2 . # _struct.entry_id 4UBY _struct.title 'Crystal structure of a polymorphic beta1 peptide' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag ? # _struct_keywords.entry_id 4UBY _struct_keywords.text 'prion peptide, de novo protein, membrane protein' _struct_keywords.pdbx_keywords 'de novo protein, membrane protein' # 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 1 ? D N N 1 ? E N N 2 ? F N N 2 ? G N N 2 ? H N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 4UBY _struct_ref.pdbx_db_accession 4UBY _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 4UBY A 1 ? 6 ? 4UBY 126 ? 131 ? 126 131 2 1 4UBY B 1 ? 6 ? 4UBY 126 ? 131 ? 126 131 3 1 4UBY C 1 ? 6 ? 4UBY 126 ? 131 ? 126 131 4 1 4UBY D 1 ? 6 ? 4UBY 126 ? 131 ? 126 131 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # 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 11.6660000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 1_565 x,y+1,z 1.0000000000 0.0000000000 0.0000000000 -0.0598472185 0.0000000000 1.0000000000 0.0000000000 17.1448955468 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 1_665 x+1,y+1,z 1.0000000000 0.0000000000 0.0000000000 11.6061527815 0.0000000000 1.0000000000 0.0000000000 17.1448955468 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # _struct_biol.details ;biological unit displays only a portion of the crystal lattice to demonstrate the crystal packing content. The crystal packing is formed by a repetition in both directions of the portion indicated in remark 350. ; _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.pdbx_formula_weight ? _struct_biol.pdbx_formula_weight_method ? _struct_biol.pdbx_aggregation_state ? _struct_biol.pdbx_assembly_method ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 2 ? AA2 ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA2 1 2 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 VAL A 4 ? LEU A 5 ? VAL A 129 LEU A 130 AA1 2 VAL B 4 ? LEU B 5 ? VAL B 129 LEU B 130 AA2 1 GLY C 2 ? LEU C 5 ? GLY C 127 LEU C 130 AA2 2 GLY D 2 ? LEU D 5 ? GLY D 127 LEU D 130 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N VAL A 4 ? N VAL A 129 O LEU B 5 ? O LEU B 130 AA2 1 2 N LEU C 5 ? N LEU C 130 O GLY D 2 ? O GLY D 127 # 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 LEU N N N N 14 LEU CA C N S 15 LEU C C N N 16 LEU O O N N 17 LEU CB C N N 18 LEU CG C N N 19 LEU CD1 C N N 20 LEU CD2 C N N 21 LEU OXT O N N 22 LEU H H N N 23 LEU H2 H N N 24 LEU HA H N N 25 LEU HB2 H N N 26 LEU HB3 H N N 27 LEU HG H N N 28 LEU HD11 H N N 29 LEU HD12 H N N 30 LEU HD13 H N N 31 LEU HD21 H N N 32 LEU HD22 H N N 33 LEU HD23 H N N 34 LEU HXT H N N 35 TYR N N N N 36 TYR CA C N S 37 TYR C C N N 38 TYR O O N N 39 TYR CB C N N 40 TYR CG C Y N 41 TYR CD1 C Y N 42 TYR CD2 C Y N 43 TYR CE1 C Y N 44 TYR CE2 C Y N 45 TYR CZ C Y N 46 TYR OH O N N 47 TYR OXT O N N 48 TYR H H N N 49 TYR H2 H N N 50 TYR HA H N N 51 TYR HB2 H N N 52 TYR HB3 H N N 53 TYR HD1 H N N 54 TYR HD2 H N N 55 TYR HE1 H N N 56 TYR HE2 H N N 57 TYR HH H N N 58 TYR HXT H N N 59 VAL N N N N 60 VAL CA C N S 61 VAL C C N N 62 VAL O O N N 63 VAL CB C N N 64 VAL CG1 C N N 65 VAL CG2 C N N 66 VAL OXT O N N 67 VAL H H N N 68 VAL H2 H N N 69 VAL HA H N N 70 VAL HB H N N 71 VAL HG11 H N N 72 VAL HG12 H N N 73 VAL HG13 H N N 74 VAL HG21 H N N 75 VAL HG22 H N N 76 VAL HG23 H N N 77 VAL HXT H N N 78 # 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 LEU N CA sing N N 12 LEU N H sing N N 13 LEU N H2 sing N N 14 LEU CA C sing N N 15 LEU CA CB sing N N 16 LEU CA HA sing N N 17 LEU C O doub N N 18 LEU C OXT sing N N 19 LEU CB CG sing N N 20 LEU CB HB2 sing N N 21 LEU CB HB3 sing N N 22 LEU CG CD1 sing N N 23 LEU CG CD2 sing N N 24 LEU CG HG sing N N 25 LEU CD1 HD11 sing N N 26 LEU CD1 HD12 sing N N 27 LEU CD1 HD13 sing N N 28 LEU CD2 HD21 sing N N 29 LEU CD2 HD22 sing N N 30 LEU CD2 HD23 sing N N 31 LEU OXT HXT sing N N 32 TYR N CA sing N N 33 TYR N H sing N N 34 TYR N H2 sing N N 35 TYR CA C sing N N 36 TYR CA CB sing N N 37 TYR CA HA sing N N 38 TYR C O doub N N 39 TYR C OXT sing N N 40 TYR CB CG sing N N 41 TYR CB HB2 sing N N 42 TYR CB HB3 sing N N 43 TYR CG CD1 doub Y N 44 TYR CG CD2 sing Y N 45 TYR CD1 CE1 sing Y N 46 TYR CD1 HD1 sing N N 47 TYR CD2 CE2 doub Y N 48 TYR CD2 HD2 sing N N 49 TYR CE1 CZ doub Y N 50 TYR CE1 HE1 sing N N 51 TYR CE2 CZ sing Y N 52 TYR CE2 HE2 sing N N 53 TYR CZ OH sing N N 54 TYR OH HH sing N N 55 TYR OXT HXT sing N N 56 VAL N CA sing N N 57 VAL N H sing N N 58 VAL N H2 sing N N 59 VAL CA C sing N N 60 VAL CA CB sing N N 61 VAL CA HA sing N N 62 VAL C O doub N N 63 VAL C OXT sing N N 64 VAL CB CG1 sing N N 65 VAL CB CG2 sing N N 66 VAL CB HB sing N N 67 VAL CG1 HG11 sing N N 68 VAL CG1 HG12 sing N N 69 VAL CG1 HG13 sing N N 70 VAL CG2 HG21 sing N N 71 VAL CG2 HG22 sing N N 72 VAL CG2 HG23 sing N N 73 VAL OXT HXT sing N N 74 # _atom_sites.entry_id 4UBY _atom_sites.fract_transf_matrix[1][1] 0.085719 _atom_sites.fract_transf_matrix[1][2] 0.000304 _atom_sites.fract_transf_matrix[1][3] -0.005370 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.058326 _atom_sites.fract_transf_matrix[2][3] -0.010574 _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] 0.053384 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O # loop_