data_1YJO # _entry.id 1YJO # _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 1YJO pdb_00001yjo 10.2210/pdb1yjo/pdb RCSB RCSB031589 ? ? WWPDB D_1000031589 ? ? # 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 2005-06-14 2 'Structure model' 1 1 2008-04-30 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-14 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Database references' 5 4 'Structure model' 'Derived calculations' # 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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_site # 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 14 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 15 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 16 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 17 4 'Structure model' '_pdbx_struct_conn_angle.value' 18 4 'Structure model' '_struct_conn.pdbx_dist_value' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr1_symmetry' 26 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 4 'Structure model' '_struct_conn.ptnr2_symmetry' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1YJO _pdbx_database_status.recvd_initial_deposition_date 2005-01-15 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 1YJP _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Nelson, R.' 1 'Sawaya, M.R.' 2 'Balbirnie, M.' 3 'Madsen, A.O.' 4 'Riekel, C.' 5 'Grothe, R.' 6 'Eisenberg, D.' 7 # _citation.id primary _citation.title 'Structure of the cross-beta spine of amyloid-like fibrils.' _citation.journal_abbrev Nature _citation.journal_volume 435 _citation.page_first 773 _citation.page_last 778 _citation.year 2005 _citation.journal_id_ASTM NATUAS _citation.country UK _citation.journal_id_ISSN 0028-0836 _citation.journal_id_CSD 0006 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15944695 _citation.pdbx_database_id_DOI 10.1038/nature03680 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Nelson, R.' 1 ? primary 'Sawaya, M.R.' 2 ? primary 'Balbirnie, M.' 3 ? primary 'Madsen, A.O.' 4 ? primary 'Riekel, C.' 5 ? primary 'Grothe, R.' 6 ? primary 'Eisenberg, D.' 7 ? # 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 'Eukaryotic peptide chain release factor GTP-binding subunit' 779.755 1 ? ? 'prion determining domain of Sup35' ? 2 non-polymer syn 'ZINC ION' 65.409 1 ? ? ? ? 3 non-polymer syn 'ACETIC ACID' 60.052 1 ? ? ? ? 4 water nat water 18.015 7 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'ERF2, Translation release factor 3, ERF3, ERF-3, Omnipotent suppressor protein 2, G1 to S phase transition protein 1' # _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 NNQQNY _entity_poly.pdbx_seq_one_letter_code_can NNQQNY _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'ZINC ION' ZN 3 'ACETIC ACID' ACY 4 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASN n 1 2 ASN n 1 3 GLN n 1 4 GLN n 1 5 ASN n 1 6 TYR 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'This sequence is from the prion determining domain of Saccharomyces cerevisiae Sup35' # 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 ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 HOH non-polymer . WATER ? 'H2 O' 18.015 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # 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 ASN 1 1 1 ASN ASN A . n A 1 2 ASN 2 2 2 ASN ASN A . n A 1 3 GLN 3 3 3 GLN GLN A . n A 1 4 GLN 4 4 4 GLN GLN A . n A 1 5 ASN 5 5 5 ASN ASN A . n A 1 6 TYR 6 6 6 TYR TYR 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 ZN 1 7 7 ZN ZN A . C 3 ACY 1 10 10 ACY ACY A . D 4 HOH 1 8 8 HOH HOH A . D 4 HOH 2 9 9 HOH HOH A . D 4 HOH 3 11 11 HOH HOH A . D 4 HOH 4 12 12 HOH HOH A . D 4 HOH 5 13 13 HOH HOH A . D 4 HOH 6 14 14 HOH HOH A . D 4 HOH 7 15 15 HOH HOH A . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0005 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 MLPHARE phasing . ? 4 # _cell.entry_id 1YJO _cell.length_a 21.153 _cell.length_b 4.870 _cell.length_c 23.130 _cell.angle_alpha 90.00 _cell.angle_beta 102.93 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YJO _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1YJO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.38 _exptl_crystal.density_percent_sol 10.32 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 7.00 _exptl_crystal_grow.pdbx_details 'ZINC SULFATE, SODIUM ACETATE, HEPES, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.00' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type MARRESEARCH _diffrn_detector.pdbx_collection_date 2004-09-22 _diffrn_detector.details 'ELLIPSOIDAL MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'CHANNEL-CUT SI-111 MONOCHROMATOR' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.975 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID13' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID13 _diffrn_source.pdbx_wavelength 0.975 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1YJO _reflns.observed_criterion_sigma_I 0.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 80.000 _reflns.d_resolution_high 1.300 _reflns.number_obs 2166 _reflns.number_all ? _reflns.percent_possible_obs 97.1 _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value 0.146 _reflns.pdbx_netI_over_sigmaI 9.8000 _reflns.B_iso_Wilson_estimate 11.70 _reflns.pdbx_redundancy 3.800 _reflns.R_free_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.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.30 _reflns_shell.d_res_low 1.40 _reflns_shell.percent_possible_all 88.8 _reflns_shell.Rmerge_I_obs ? _reflns_shell.pdbx_Rsym_value 0.426 _reflns_shell.meanI_over_sigI_obs 2.600 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1YJO _refine.ls_number_reflns_obs 1250 _refine.ls_number_reflns_all 1250 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 22.54 _refine.ls_d_res_high 1.30 _refine.ls_percent_reflns_obs 97.9 _refine.ls_R_factor_obs 0.103 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.102 _refine.ls_R_factor_R_free 0.152 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.000 _refine.ls_number_reflns_R_free 52 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.985 _refine.correlation_coeff_Fo_to_Fc_free 0.960 _refine.B_iso_mean 5.76 _refine.aniso_B[1][1] -0.16000 _refine.aniso_B[2][2] -0.44000 _refine.aniso_B[3][3] 0.73000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.28000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details MASK _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.043 _refine.pdbx_overall_ESU_R_Free 0.047 _refine.overall_SU_ML 0.025 _refine.overall_SU_B 1.463 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 55 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 1 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 67 _refine_hist.d_res_high 1.30 _refine_hist.d_res_low 22.54 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.007 0.021 ? 58 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 37 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.077 1.892 ? 77 'X-RAY DIFFRACTION' ? r_angle_other_deg 0.728 3.000 ? 88 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 8.504 5.000 ? 5 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 59.937 28.333 ? 6 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 9.092 15.000 ? 8 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_chiral_restr 0.092 0.200 ? 6 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.004 0.020 ? 71 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.000 0.020 ? 9 'X-RAY DIFFRACTION' ? r_nbd_refined 0.225 0.200 ? 4 'X-RAY DIFFRACTION' ? r_nbd_other 0.187 0.200 ? 20 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.194 0.200 ? 18 'X-RAY DIFFRACTION' ? r_nbtor_other 0.083 0.200 ? 33 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.219 0.200 ? 4 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined 0.039 0.200 ? 2 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.171 0.200 ? 6 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.339 0.200 ? 13 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.181 0.200 ? 4 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined 0.016 0.200 ? 1 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.663 1.500 ? 43 'X-RAY DIFFRACTION' ? r_mcbond_other 0.228 1.500 ? 14 'X-RAY DIFFRACTION' ? r_mcangle_it 0.895 2.000 ? 49 'X-RAY DIFFRACTION' ? r_scbond_it 1.394 3.000 ? 33 'X-RAY DIFFRACTION' ? r_scangle_it 1.715 4.500 ? 28 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.30 _refine_ls_shell.d_res_low 1.33 _refine_ls_shell.number_reflns_R_work 76 _refine_ls_shell.R_factor_R_work 0.012 _refine_ls_shell.percent_reflns_obs 87.10 _refine_ls_shell.R_factor_R_free 0.0135 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 5 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _database_PDB_matrix.entry_id 1YJO _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1YJO _struct.title 'Structure of NNQQNY from yeast prion Sup35 with zinc acetate' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1YJO _struct_keywords.pdbx_keywords 'PROTEIN BINDING' _struct_keywords.text 'Keywords beta sheet, steric zipper, glutamine zipper, asparagine zipper, PROTEIN BINDING' # 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 ? C N N 3 ? D N N 4 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code ERF2_YEAST _struct_ref.pdbx_db_accession P05453 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code NNQQNY _struct_ref.pdbx_align_begin 8 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1YJO _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 P05453 _struct_ref_seq.db_align_beg 8 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 13 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D # 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' 2_555 -x,y+1/2,-z -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2.4350000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role metalc1 metalc ? ? A ASN 1 N ? ? ? 1_655 B ZN . ZN ? ? A ASN 1 A ZN 7 1_555 ? ? ? ? ? ? ? 2.119 ? ? metalc2 metalc ? ? A TYR 6 O ? ? ? 1_555 B ZN . ZN ? ? A TYR 6 A ZN 7 1_555 ? ? ? ? ? ? ? 2.014 ? ? metalc3 metalc ? ? A TYR 6 OXT ? ? ? 1_555 B ZN . ZN ? ? A TYR 6 A ZN 7 1_555 ? ? ? ? ? ? ? 2.715 ? ? metalc4 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACY . OXT ? ? A ZN 7 A ACY 10 1_555 ? ? ? ? ? ? ? 1.964 ? ? metalc5 metalc ? ? B ZN . ZN ? ? ? 1_555 C ACY . O ? ? A ZN 7 A ACY 10 1_545 ? ? ? ? ? ? ? 2.005 ? ? metalc6 metalc ? ? B ZN . ZN ? ? ? 1_565 C ACY . O ? ? A ZN 7 A ACY 10 1_555 ? ? ? ? ? ? ? 2.005 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 N ? A ASN 1 ? A ASN 1 ? 1_655 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? A TYR 6 ? A TYR 6 ? 1_555 102.5 ? 2 N ? A ASN 1 ? A ASN 1 ? 1_655 ZN ? B ZN . ? A ZN 7 ? 1_555 OXT ? A TYR 6 ? A TYR 6 ? 1_555 153.2 ? 3 O ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 OXT ? A TYR 6 ? A TYR 6 ? 1_555 50.9 ? 4 N ? A ASN 1 ? A ASN 1 ? 1_655 ZN ? B ZN . ? A ZN 7 ? 1_555 OXT ? C ACY . ? A ACY 10 ? 1_555 104.3 ? 5 O ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 OXT ? C ACY . ? A ACY 10 ? 1_555 112.4 ? 6 OXT ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 OXT ? C ACY . ? A ACY 10 ? 1_555 86.6 ? 7 N ? A ASN 1 ? A ASN 1 ? 1_655 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_545 112.3 ? 8 O ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_545 113.7 ? 9 OXT ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_545 85.3 ? 10 OXT ? C ACY . ? A ACY 10 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_545 111.0 ? 11 N ? A ASN 1 ? A ASN 1 ? 1_655 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_555 109.5 ? 12 O ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_555 118.9 ? 13 OXT ? A TYR 6 ? A TYR 6 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_555 85.6 ? 14 OXT ? C ACY . ? A ACY 10 ? 1_555 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_555 10.6 ? 15 O ? C ACY . ? A ACY 10 ? 1_545 ZN ? B ZN . ? A ZN 7 ? 1_555 O ? C ACY . ? A ACY 10 ? 1_555 100.3 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A ZN 7 ? 4 'BINDING SITE FOR RESIDUE ZN A 7' AC2 Software A ACY 10 ? 7 'BINDING SITE FOR RESIDUE ACY A 10' # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 4 ASN A 1 ? ASN A 1 . ? 1_655 ? 2 AC1 4 TYR A 6 ? TYR A 6 . ? 1_555 ? 3 AC1 4 ACY C . ? ACY A 10 . ? 1_555 ? 4 AC1 4 ACY C . ? ACY A 10 . ? 1_545 ? 5 AC2 7 ASN A 1 ? ASN A 1 . ? 1_665 ? 6 AC2 7 ASN A 1 ? ASN A 1 . ? 1_655 ? 7 AC2 7 ASN A 2 ? ASN A 2 . ? 1_665 ? 8 AC2 7 TYR A 6 ? TYR A 6 . ? 1_555 ? 9 AC2 7 TYR A 6 ? TYR A 6 . ? 1_565 ? 10 AC2 7 ZN B . ? ZN A 7 . ? 1_565 ? 11 AC2 7 ZN B . ? ZN A 7 . ? 1_555 ? # _pdbx_database_remark.id 300 _pdbx_database_remark.text ;BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). The second beta strand of the beta sandwich is generated as described in remark 350. Beta sheets are generated from unit cell translations along the unit cell b dimension: x,y+1,z. ; # 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 ACY C C N N 1 ACY O O N N 2 ACY OXT O N N 3 ACY CH3 C N N 4 ACY HXT H N N 5 ACY H1 H N N 6 ACY H2 H N N 7 ACY H3 H N N 8 ASN N N N N 9 ASN CA C N S 10 ASN C C N N 11 ASN O O N N 12 ASN CB C N N 13 ASN CG C N N 14 ASN OD1 O N N 15 ASN ND2 N N N 16 ASN OXT O N N 17 ASN H H N N 18 ASN H2 H N N 19 ASN HA H N N 20 ASN HB2 H N N 21 ASN HB3 H N N 22 ASN HD21 H N N 23 ASN HD22 H N N 24 ASN HXT H N N 25 GLN N N N N 26 GLN CA C N S 27 GLN C C N N 28 GLN O O N N 29 GLN CB C N N 30 GLN CG C N N 31 GLN CD C N N 32 GLN OE1 O N N 33 GLN NE2 N N N 34 GLN OXT O N N 35 GLN H H N N 36 GLN H2 H N N 37 GLN HA H N N 38 GLN HB2 H N N 39 GLN HB3 H N N 40 GLN HG2 H N N 41 GLN HG3 H N N 42 GLN HE21 H N N 43 GLN HE22 H N N 44 GLN HXT H N N 45 HOH O O N N 46 HOH H1 H N N 47 HOH H2 H N N 48 TYR N N N N 49 TYR CA C N S 50 TYR C C N N 51 TYR O O N N 52 TYR CB C N N 53 TYR CG C Y N 54 TYR CD1 C Y N 55 TYR CD2 C Y N 56 TYR CE1 C Y N 57 TYR CE2 C Y N 58 TYR CZ C Y N 59 TYR OH O N N 60 TYR OXT O N N 61 TYR H H N N 62 TYR H2 H N N 63 TYR HA H N N 64 TYR HB2 H N N 65 TYR HB3 H N N 66 TYR HD1 H N N 67 TYR HD2 H N N 68 TYR HE1 H N N 69 TYR HE2 H N N 70 TYR HH H N N 71 TYR HXT H N N 72 ZN ZN ZN N N 73 # 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 ACY C O doub N N 1 ACY C OXT sing N N 2 ACY C CH3 sing N N 3 ACY OXT HXT sing N N 4 ACY CH3 H1 sing N N 5 ACY CH3 H2 sing N N 6 ACY CH3 H3 sing N N 7 ASN N CA sing N N 8 ASN N H sing N N 9 ASN N H2 sing N N 10 ASN CA C sing N N 11 ASN CA CB sing N N 12 ASN CA HA sing N N 13 ASN C O doub N N 14 ASN C OXT sing N N 15 ASN CB CG sing N N 16 ASN CB HB2 sing N N 17 ASN CB HB3 sing N N 18 ASN CG OD1 doub N N 19 ASN CG ND2 sing N N 20 ASN ND2 HD21 sing N N 21 ASN ND2 HD22 sing N N 22 ASN OXT HXT sing N N 23 GLN N CA sing N N 24 GLN N H sing N N 25 GLN N H2 sing N N 26 GLN CA C sing N N 27 GLN CA CB sing N N 28 GLN CA HA sing N N 29 GLN C O doub N N 30 GLN C OXT sing N N 31 GLN CB CG sing N N 32 GLN CB HB2 sing N N 33 GLN CB HB3 sing N N 34 GLN CG CD sing N N 35 GLN CG HG2 sing N N 36 GLN CG HG3 sing N N 37 GLN CD OE1 doub N N 38 GLN CD NE2 sing N N 39 GLN NE2 HE21 sing N N 40 GLN NE2 HE22 sing N N 41 GLN OXT HXT sing N N 42 HOH O H1 sing N N 43 HOH O H2 sing N N 44 TYR N CA sing N N 45 TYR N H sing N N 46 TYR N H2 sing N N 47 TYR CA C sing N N 48 TYR CA CB sing N N 49 TYR CA HA sing N N 50 TYR C O doub N N 51 TYR C OXT sing N N 52 TYR CB CG sing N N 53 TYR CB HB2 sing N N 54 TYR CB HB3 sing N N 55 TYR CG CD1 doub Y N 56 TYR CG CD2 sing Y N 57 TYR CD1 CE1 sing Y N 58 TYR CD1 HD1 sing N N 59 TYR CD2 CE2 doub Y N 60 TYR CD2 HD2 sing N N 61 TYR CE1 CZ doub Y N 62 TYR CE1 HE1 sing N N 63 TYR CE2 CZ sing Y N 64 TYR CE2 HE2 sing N N 65 TYR CZ OH sing N N 66 TYR OH HH sing N N 67 TYR OXT HXT sing N N 68 # _atom_sites.entry_id 1YJO _atom_sites.fract_transf_matrix[1][1] 0.047275 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.010853 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.205339 _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] 0.044359 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O ZN # loop_