data_4TUT # _entry.id 4TUT # _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 4TUT pdb_00004tut 10.2210/pdb4tut/pdb WWPDB D_1000202259 ? ? # 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 2015-07-01 3 'Structure model' 1 2 2017-11-22 4 'Structure model' 1 3 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' 'Structure summary' 2 3 'Structure model' 'Database references' 3 3 'Structure model' 'Derived calculations' 4 3 'Structure model' 'Refinement description' 5 3 'Structure model' 'Source and taxonomy' 6 4 'Structure model' 'Data collection' 7 4 'Structure model' 'Database references' 8 4 'Structure model' 'Experimental preparation' # 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 3 'Structure model' citation 2 3 'Structure model' pdbx_entity_src_syn 3 3 'Structure model' pdbx_struct_oper_list 4 3 'Structure model' software 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 'Structure model' database_2 8 4 'Structure model' exptl_crystal # 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 3 'Structure model' '_citation.journal_id_CSD' 2 3 'Structure model' '_pdbx_entity_src_syn.pdbx_alt_source_flag' 3 3 'Structure model' '_pdbx_struct_oper_list.symmetry_operation' 4 4 'Structure model' '_database_2.pdbx_DOI' 5 4 'Structure model' '_database_2.pdbx_database_accession' 6 4 'Structure model' '_exptl_crystal.density_Matthews' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 4TUT _pdbx_database_status.recvd_initial_deposition_date 2014-06-24 _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 4UBY PDB . 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 . # 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: GLY-GLY-TYR-MET-LEU-GLY' 596.698 1 ? ? ? ? 2 water nat water 18.015 5 ? ? ? ? # _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 GGYMLG _entity_poly.pdbx_seq_one_letter_code_can GGYMLG _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 GLY n 1 3 TYR n 1 4 MET 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 # 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 MET 4 129 129 MET MET A . n A 1 5 LEU 5 130 130 LEU LEU A . n A 1 6 GLY 6 131 131 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 1 201 4 HOH HOH A . B 2 HOH 2 202 3 HOH HOH A . B 2 HOH 3 203 1 HOH HOH A . B 2 HOH 4 204 5 HOH HOH A . B 2 HOH 5 205 2 HOH HOH A . # loop_ _software.citation_id _software.classification _software.compiler_name _software.compiler_version _software.contact_author _software.contact_author_email _software.date _software.description _software.dependencies _software.hardware _software.language _software.location _software.mods _software.name _software.os _software.os_version _software.type _software.version _software.pdbx_ordinal ? refinement ? ? ? ? ? ? ? ? ? ? ? PHENIX ? ? ? '(phenix.refine: 1.9_1692)' 1 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? HKL-3000 ? ? ? . 2 ? 'data extraction' ? ? ? ? ? ? ? ? ? ? ? PDB_EXTRACT ? ? ? 3.14 3 ? 'data reduction' ? ? ? ? ? ? ? ? ? ? ? DENZO ? ? ? . 4 ? 'data scaling' ? ? ? ? ? ? ? ? ? ? ? SCALEPACK ? ? ? . 5 # _cell.length_a 10.395 _cell.length_b 9.731 _cell.length_c 17.382 _cell.angle_alpha 90.000 _cell.angle_beta 105.940 _cell.angle_gamma 90.000 _cell.entry_id 4TUT _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.entry_id 4TUT _symmetry.Int_Tables_number 4 _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 4TUT _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 1.42 _exptl_crystal.density_method ? _exptl_crystal.density_percent_sol ? _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 6.5 _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 cacodylate pH 6.5, 1.3 M sodium acetate, and 25 % ethylene glycol' _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 2010-11-18 # _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 0.72932 _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-D' _diffrn_source.voltage ? _diffrn_source.take-off_angle ? _diffrn_source.pdbx_wavelength_list 0.72932 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_beamline 23-ID-D _diffrn_source.pdbx_synchrotron_site APS # _reflns.entry_id 4TUT _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.d_resolution_high 0.900 _reflns.d_resolution_low 50.000 _reflns.pdbx_number_measured_all 7403 _reflns.number_obs 1862 _reflns.pdbx_Rmerge_I_obs 0.066 _reflns.pdbx_netI_over_av_sigmaI 20.908 _reflns.pdbx_netI_over_sigmaI 27.400 _reflns.pdbx_chi_squared 1.019 _reflns.pdbx_redundancy 4.000 _reflns.percent_possible_obs 71.400 _reflns.B_iso_Wilson_estimate 1.550 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? # 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 0.900 0.930 ? ? ? 0 0.068 ? ? 1.047 1.900 ? ? ? 82 ? ? ? ? 32.300 ? ? ? 1 2 0.930 0.970 ? ? ? 0 0.070 ? ? 1.055 2.400 ? ? ? 130 ? ? ? ? 48.300 ? ? ? 1 3 0.970 1.010 ? ? ? 0 0.068 ? ? 1.035 2.800 ? ? ? 135 ? ? ? ? 56.500 ? ? ? 1 4 1.010 1.070 ? ? ? 0 0.070 ? ? 1.028 3.100 ? ? ? 165 ? ? ? ? 64.500 ? ? ? 1 5 1.070 1.130 ? ? ? 0 0.060 ? ? 1.027 3.600 ? ? ? 202 ? ? ? ? 77.700 ? ? ? 1 6 1.130 1.220 ? ? ? 0 0.059 ? ? 1.019 3.900 ? ? ? 209 ? ? ? ? 80.400 ? ? ? 1 7 1.220 1.340 ? ? ? 0 0.068 ? ? 1.021 4.200 ? ? ? 212 ? ? ? ? 80.300 ? ? ? 1 8 1.340 1.540 ? ? ? 0 0.068 ? ? 1.041 4.500 ? ? ? 230 ? ? ? ? 87.100 ? ? ? 1 9 1.540 1.940 ? ? ? 0 0.067 ? ? 0.968 4.900 ? ? ? 237 ? ? ? ? 90.500 ? ? ? 1 10 1.940 50.000 ? ? ? 0 0.067 ? ? 1.027 5.400 ? ? ? 260 ? ? ? ? 92.500 ? ? ? # _refine.entry_id 4TUT _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.ls_d_res_high 0.9000 _refine.ls_d_res_low 9.9960 _refine.pdbx_ls_sigma_F 2.320 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 71.4800 _refine.ls_number_reflns_obs 1860 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method 'FREE R-VALUE' _refine.ls_matrix_type ? _refine.pdbx_R_Free_selection_details 'Random selection' _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.0712 _refine.ls_R_factor_R_work 0.0700 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.0980 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.3000 _refine.ls_number_reflns_R_free 80 _refine.ls_number_reflns_R_work 1780 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 2.4970 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _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 ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.0300 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.1100 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'AB INITIO PHASING' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 12.320 _refine.B_iso_min 1.310 _refine.pdbx_overall_phase_error 6.3000 _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 0.9000 _refine_hist.d_res_low 9.9960 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 5 _refine_hist.number_atoms_total 46 _refine_hist.pdbx_number_residues_total 6 _refine_hist.pdbx_B_iso_mean_solvent 7.70 _refine_hist.pdbx_number_atoms_protein 41 _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' f_bond_d 41 0.007 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 53 1.365 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 4 0.058 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 7 0.010 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 14 6.074 ? ? ? # _refine_ls_shell.d_res_high 0.8996 _refine_ls_shell.d_res_low ? _refine_ls_shell.pdbx_total_number_of_bins_used 1 _refine_ls_shell.percent_reflns_obs 71.0000 _refine_ls_shell.number_reflns_R_work 1780 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.0700 _refine_ls_shell.R_factor_R_free 0.0980 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 80 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 1860 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_obs ? # _struct.entry_id 4TUT _struct.title 'Structure of a Prion 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 4TUT _struct_keywords.text 'prion peptide, MEMBRANE PROTEIN, DE NOVO PROTEIN' _struct_keywords.pdbx_keywords 'MEMBRANE PROTEIN, DE NOVO 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 2 ? # _struct_ref.db_code 4TUT _struct_ref.db_name PDB _struct_ref.details ? _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.seq_align ? _struct_ref.seq_dif ? _struct_ref.pdbx_db_accession 4TUT _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_align_end ? _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4TUT _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 4TUT _struct_ref_seq.db_align_beg 126 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 131 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 126 _struct_ref_seq.pdbx_auth_seq_align_end 131 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 880 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # _struct_biol.details 'biological unit is the same as asym.' _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_ _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 MET N N N N 36 MET CA C N S 37 MET C C N N 38 MET O O N N 39 MET CB C N N 40 MET CG C N N 41 MET SD S N N 42 MET CE C N N 43 MET OXT O N N 44 MET H H N N 45 MET H2 H N N 46 MET HA H N N 47 MET HB2 H N N 48 MET HB3 H N N 49 MET HG2 H N N 50 MET HG3 H N N 51 MET HE1 H N N 52 MET HE2 H N N 53 MET HE3 H N N 54 MET HXT H N N 55 TYR N N N N 56 TYR CA C N S 57 TYR C C N N 58 TYR O O N N 59 TYR CB C N N 60 TYR CG C Y N 61 TYR CD1 C Y N 62 TYR CD2 C Y N 63 TYR CE1 C Y N 64 TYR CE2 C Y N 65 TYR CZ C Y N 66 TYR OH O N N 67 TYR OXT O N N 68 TYR H H N N 69 TYR H2 H N N 70 TYR HA H N N 71 TYR HB2 H N N 72 TYR HB3 H N N 73 TYR HD1 H N N 74 TYR HD2 H N N 75 TYR HE1 H N N 76 TYR HE2 H N N 77 TYR HH H N N 78 TYR HXT H N N 79 # 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 MET N CA sing N N 33 MET N H sing N N 34 MET N H2 sing N N 35 MET CA C sing N N 36 MET CA CB sing N N 37 MET CA HA sing N N 38 MET C O doub N N 39 MET C OXT sing N N 40 MET CB CG sing N N 41 MET CB HB2 sing N N 42 MET CB HB3 sing N N 43 MET CG SD sing N N 44 MET CG HG2 sing N N 45 MET CG HG3 sing N N 46 MET SD CE sing N N 47 MET CE HE1 sing N N 48 MET CE HE2 sing N N 49 MET CE HE3 sing N N 50 MET OXT HXT sing N N 51 TYR N CA sing N N 52 TYR N H sing N N 53 TYR N H2 sing N N 54 TYR CA C sing N N 55 TYR CA CB sing N N 56 TYR CA HA sing N N 57 TYR C O doub N N 58 TYR C OXT sing N N 59 TYR CB CG sing N N 60 TYR CB HB2 sing N N 61 TYR CB HB3 sing N N 62 TYR CG CD1 doub Y N 63 TYR CG CD2 sing Y N 64 TYR CD1 CE1 sing Y N 65 TYR CD1 HD1 sing N N 66 TYR CD2 CE2 doub Y N 67 TYR CD2 HD2 sing N N 68 TYR CE1 CZ doub Y N 69 TYR CE1 HE1 sing N N 70 TYR CE2 CZ sing Y N 71 TYR CE2 HE2 sing N N 72 TYR CZ OH sing N N 73 TYR OH HH sing N N 74 TYR OXT HXT sing N N 75 # _atom_sites.entry_id 4TUT _atom_sites.fract_transf_matrix[1][1] 0.096200 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.027469 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.102764 _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] 0.059830 _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 H N O S # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . GLY A 1 1 ? 17.293 1.560 23.968 1.00 2.01 ? 126 GLY A N 1 ATOM 2 C CA . GLY A 1 1 ? 16.849 0.827 22.791 1.00 1.95 ? 126 GLY A CA 1 ATOM 3 C C . GLY A 1 1 ? 15.759 1.608 22.098 1.00 2.10 ? 126 GLY A C 1 ATOM 4 O O . GLY A 1 1 ? 15.565 2.786 22.386 1.00 2.85 ? 126 GLY A O 1 ATOM 5 N N . GLY A 1 2 ? 15.042 0.968 21.186 1.00 1.73 ? 127 GLY A N 1 ATOM 6 C CA . GLY A 1 2 ? 14.034 1.688 20.438 1.00 1.89 ? 127 GLY A CA 1 ATOM 7 C C . GLY A 1 2 ? 13.225 0.763 19.570 1.00 1.67 ? 127 GLY A C 1 ATOM 8 O O . GLY A 1 2 ? 13.387 -0.455 19.626 1.00 1.89 ? 127 GLY A O 1 ATOM 9 N N . TYR A 1 3 ? 12.346 1.343 18.764 1.00 1.31 ? 128 TYR A N 1 ATOM 10 C CA . TYR A 1 3 ? 11.429 0.542 17.964 1.00 1.33 ? 128 TYR A CA 1 ATOM 11 C C . TYR A 1 3 ? 10.906 1.404 16.824 1.00 1.35 ? 128 TYR A C 1 ATOM 12 O O . TYR A 1 3 ? 10.959 2.642 16.877 1.00 1.38 ? 128 TYR A O 1 ATOM 13 C CB . TYR A 1 3 ? 10.261 -0.015 18.826 1.00 1.46 ? 128 TYR A CB 1 ATOM 14 C CG . TYR A 1 3 ? 9.455 1.105 19.430 1.00 1.53 ? 128 TYR A CG 1 ATOM 15 C CD1 . TYR A 1 3 ? 9.869 1.725 20.609 1.00 1.71 ? 128 TYR A CD1 1 ATOM 16 C CD2 . TYR A 1 3 ? 8.325 1.603 18.782 1.00 1.82 ? 128 TYR A CD2 1 ATOM 17 C CE1 . TYR A 1 3 ? 9.179 2.805 21.129 1.00 1.85 ? 128 TYR A CE1 1 ATOM 18 C CE2 . TYR A 1 3 ? 7.628 2.681 19.297 1.00 2.07 ? 128 TYR A CE2 1 ATOM 19 C CZ . TYR A 1 3 ? 8.063 3.280 20.464 1.00 2.25 ? 128 TYR A CZ 1 ATOM 20 O OH . TYR A 1 3 ? 7.374 4.361 20.943 1.00 2.82 ? 128 TYR A OH 1 ATOM 21 N N . MET A 1 4 ? 10.393 0.725 15.804 1.00 1.48 ? 129 MET A N 1 ATOM 22 C CA . MET A 1 4 ? 9.886 1.367 14.602 1.00 1.42 ? 129 MET A CA 1 ATOM 23 C C . MET A 1 4 ? 8.529 0.778 14.227 1.00 1.41 ? 129 MET A C 1 ATOM 24 O O . MET A 1 4 ? 8.331 -0.445 14.303 1.00 1.48 ? 129 MET A O 1 ATOM 25 C CB . MET A 1 4 ? 10.878 1.204 13.444 1.00 1.64 ? 129 MET A CB 1 ATOM 26 C CG . MET A 1 4 ? 10.389 1.773 12.116 1.00 2.05 ? 129 MET A CG 1 ATOM 27 S SD . MET A 1 4 ? 11.651 1.731 10.822 1.00 2.53 ? 129 MET A SD 1 ATOM 28 C CE . MET A 1 4 ? 12.712 3.096 11.307 1.00 2.77 ? 129 MET A CE 1 ATOM 29 N N . LEU A 1 5 ? 7.616 1.675 13.845 1.00 1.31 ? 130 LEU A N 1 ATOM 30 C CA . LEU A 1 5 ? 6.288 1.336 13.342 1.00 1.44 ? 130 LEU A CA 1 ATOM 31 C C . LEU A 1 5 ? 6.201 1.705 11.865 1.00 1.51 ? 130 LEU A C 1 ATOM 32 O O . LEU A 1 5 ? 6.332 2.883 11.515 1.00 1.82 ? 130 LEU A O 1 ATOM 33 C CB . LEU A 1 5 ? 5.197 2.088 14.105 1.00 1.84 ? 130 LEU A CB 1 ATOM 34 C CG . LEU A 1 5 ? 5.200 2.010 15.632 1.00 2.34 ? 130 LEU A CG 1 ATOM 35 C CD1 . LEU A 1 5 ? 4.039 2.827 16.150 1.00 2.68 ? 130 LEU A CD1 1 ATOM 36 C CD2 . LEU A 1 5 ? 5.101 0.573 16.118 1.00 2.98 ? 130 LEU A CD2 1 ATOM 37 N N . GLY A 1 6 ? 5.968 0.709 11.012 1.00 1.62 ? 131 GLY A N 1 ATOM 38 C CA . GLY A 1 6 ? 5.756 0.943 9.595 1.00 1.77 ? 131 GLY A CA 1 ATOM 39 C C . GLY A 1 6 ? 4.389 0.496 9.111 1.00 1.61 ? 131 GLY A C 1 ATOM 40 O O . GLY A 1 6 ? 3.739 -0.348 9.757 1.00 1.63 ? 131 GLY A O 1 ATOM 41 O OXT . GLY A 1 6 ? 3.958 0.976 8.049 1.00 2.06 ? 131 GLY A OXT 1 HETATM 42 O O . HOH B 2 . ? 8.283 3.636 9.679 1.00 7.45 ? 201 HOH A O 1 HETATM 43 O O . HOH B 2 . ? 14.752 1.268 25.186 1.00 9.38 ? 202 HOH A O 1 HETATM 44 O O . HOH B 2 . ? 17.268 -1.078 25.446 1.00 2.59 ? 203 HOH A O 1 HETATM 45 O O . HOH B 2 . ? 12.656 4.005 23.452 1.00 12.32 ? 204 HOH A O 1 HETATM 46 O O . HOH B 2 . ? 12.047 1.052 23.073 1.00 6.76 ? 205 HOH A O 1 # loop_ _atom_site_anisotrop.id _atom_site_anisotrop.type_symbol _atom_site_anisotrop.pdbx_label_atom_id _atom_site_anisotrop.pdbx_label_alt_id _atom_site_anisotrop.pdbx_label_comp_id _atom_site_anisotrop.pdbx_label_asym_id _atom_site_anisotrop.pdbx_label_seq_id _atom_site_anisotrop.pdbx_PDB_ins_code _atom_site_anisotrop.U[1][1] _atom_site_anisotrop.U[2][2] _atom_site_anisotrop.U[3][3] _atom_site_anisotrop.U[1][2] _atom_site_anisotrop.U[1][3] _atom_site_anisotrop.U[2][3] _atom_site_anisotrop.pdbx_auth_seq_id _atom_site_anisotrop.pdbx_auth_comp_id _atom_site_anisotrop.pdbx_auth_asym_id _atom_site_anisotrop.pdbx_auth_atom_id 1 N N . GLY A 1 ? 0.0313 0.0224 0.0226 -0.0027 -0.0143 -0.0011 126 GLY A N 2 C CA . GLY A 1 ? 0.0291 0.0224 0.0226 -0.0026 -0.0149 -0.0003 126 GLY A CA 3 C C . GLY A 1 ? 0.0309 0.0224 0.0265 -0.0016 -0.0149 -0.0006 126 GLY A C 4 O O . GLY A 1 ? 0.0453 0.0279 0.0352 0.0003 -0.0231 -0.0037 126 GLY A O 5 N N . GLY A 2 ? 0.0232 0.0206 0.0219 0.0024 -0.0133 -0.0002 127 GLY A N 6 C CA . GLY A 2 ? 0.0261 0.0210 0.0247 0.0017 -0.0147 -0.0014 127 GLY A CA 7 C C . GLY A 2 ? 0.0224 0.0151 0.0259 0.0013 -0.0065 -0.0009 127 GLY A C 8 O O . GLY A 2 ? 0.0285 0.0123 0.0312 0.0044 -0.0068 -0.0023 127 GLY A O 9 N N . TYR A 3 ? 0.0142 0.0137 0.0219 -0.0018 -0.0046 -0.0011 128 TYR A N 10 C CA . TYR A 3 ? 0.0144 0.0142 0.0220 0.0003 -0.0040 -0.0007 128 TYR A CA 11 C C . TYR A 3 ? 0.0122 0.0175 0.0217 0.0012 -0.0035 0.0015 128 TYR A C 12 O O . TYR A 3 ? 0.0159 0.0168 0.0198 0.0019 -0.0044 0.0001 128 TYR A O 13 C CB . TYR A 3 ? 0.0183 0.0131 0.0241 0.0005 0.0003 0.0022 128 TYR A CB 14 C CG . TYR A 3 ? 0.0188 0.0173 0.0219 -0.0031 0.0020 0.0056 128 TYR A CG 15 C CD1 . TYR A 3 ? 0.0207 0.0224 0.0220 0.0022 0.0051 0.0060 128 TYR A CD1 16 C CD2 . TYR A 3 ? 0.0210 0.0233 0.0250 0.0019 0.0030 0.0045 128 TYR A CD2 17 C CE1 . TYR A 3 ? 0.0247 0.0235 0.0220 0.0071 0.0063 0.0062 128 TYR A CE1 18 C CE2 . TYR A 3 ? 0.0265 0.0266 0.0253 0.0071 0.0045 0.0039 128 TYR A CE2 19 C CZ . TYR A 3 ? 0.0318 0.0295 0.0241 0.0123 0.0077 0.0054 128 TYR A CZ 20 O OH . TYR A 3 ? 0.0427 0.0387 0.0257 0.0199 0.0088 -0.0017 128 TYR A OH 21 N N . MET A 4 ? 0.0163 0.0204 0.0194 0.0004 -0.0057 -0.0017 129 MET A N 22 C CA . MET A 4 ? 0.0162 0.0207 0.0170 0.0001 -0.0040 -0.0005 129 MET A CA 23 C C . MET A 4 ? 0.0168 0.0178 0.0190 -0.0001 -0.0022 0.0000 129 MET A C 24 O O . MET A 4 ? 0.0191 0.0145 0.0225 -0.0026 -0.0049 -0.0003 129 MET A O 25 C CB . MET A 4 ? 0.0188 0.0264 0.0169 0.0022 0.0030 -0.0016 129 MET A CB 26 C CG . MET A 4 ? 0.0252 0.0321 0.0207 -0.0032 0.0093 -0.0037 129 MET A CG 27 S SD . MET A 4 ? 0.0341 0.0335 0.0286 -0.0067 0.0148 -0.0075 129 MET A SD 28 C CE . MET A 4 ? 0.0340 0.0395 0.0317 -0.0087 0.0092 -0.0058 129 MET A CE 29 N N . LEU A 5 ? 0.0126 0.0187 0.0186 -0.0006 -0.0051 -0.0011 130 LEU A N 30 C CA . LEU A 5 ? 0.0142 0.0189 0.0216 -0.0025 -0.0059 -0.0009 130 LEU A CA 31 C C . LEU A 5 ? 0.0146 0.0195 0.0232 -0.0024 -0.0070 0.0012 130 LEU A C 32 O O . LEU A 5 ? 0.0247 0.0189 0.0257 -0.0020 -0.0079 0.0051 130 LEU A O 33 C CB . LEU A 5 ? 0.0203 0.0259 0.0238 0.0020 0.0001 0.0000 130 LEU A CB 34 C CG . LEU A 5 ? 0.0291 0.0311 0.0288 0.0033 0.0088 -0.0026 130 LEU A CG 35 C CD1 . LEU A 5 ? 0.0333 0.0359 0.0328 0.0012 0.0137 0.0000 130 LEU A CD1 36 C CD2 . LEU A 5 ? 0.0460 0.0343 0.0330 0.0049 0.0133 0.0001 130 LEU A CD2 37 N N . GLY A 6 ? 0.0167 0.0237 0.0210 -0.0014 -0.0060 0.0009 131 GLY A N 38 C CA . GLY A 6 ? 0.0196 0.0278 0.0201 -0.0014 -0.0062 0.0022 131 GLY A CA 39 C C . GLY A 6 ? 0.0189 0.0201 0.0222 -0.0029 -0.0053 0.0022 131 GLY A C 40 O O . GLY A 6 ? 0.0175 0.0197 0.0248 -0.0024 -0.0018 0.0056 131 GLY A O 41 O OXT . GLY A 6 ? 0.0262 0.0282 0.0238 -0.0047 -0.0077 0.0043 131 GLY A OXT 42 O O . HOH B . ? 0.0539 0.1301 0.0992 -0.0259 0.0009 0.0436 201 HOH A O 43 O O . HOH B . ? 0.0729 0.2009 0.0828 -0.0438 0.0167 -0.0559 202 HOH A O 44 O O . HOH B . ? 0.0357 0.0213 0.0414 -0.0009 -0.0097 0.0024 203 HOH A O 45 O O . HOH B . ? 0.0944 0.1896 0.1840 -0.0592 -0.0066 0.0236 204 HOH A O 46 O O . HOH B . ? 0.0937 0.1124 0.0507 0.0190 0.0229 0.0223 205 HOH A O #