data_7F29 # _entry.id 7F29 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.359 _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 7F29 pdb_00007f29 10.2210/pdb7f29/pdb WWPDB D_1300022621 ? ? EMDB EMD-31428 ? ? # _pdbx_database_related.db_name EMDB _pdbx_database_related.details . _pdbx_database_related.db_id EMD-31428 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 7F29 _pdbx_database_status.recvd_initial_deposition_date 2021-06-10 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Xia, W.C.' 1 ? 'Sun, Y.P.' 2 ? 'Liu, C.' 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 J.Am.Chem.Soc. _citation.journal_id_ASTM JACSAT _citation.journal_id_CSD ? _citation.journal_id_ISSN 1520-5126 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 143 _citation.language ? _citation.page_first 20216 _citation.page_last 20223 _citation.title 'O-Glycosylation Induces Amyloid-beta To Form New Fibril Polymorphs Vulnerable for Degradation' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/jacs.1c08607 _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Liu, D.' 1 ? primary 'Wei, Q.' 2 ? primary 'Xia, W.' 3 ? primary 'He, C.' 4 ? primary 'Zhang, Q.' 5 ? primary 'Huang, L.' 6 ? primary 'Wang, X.' 7 ? primary 'Sun, Y.' 8 ? primary 'Ma, Y.' 9 ? primary 'Zhang, X.' 10 ? primary 'Wang, Y.' 11 ? primary 'Shi, X.' 12 ? primary 'Liu, C.' 13 ? primary 'Dong, S.' 14 ? # _cell.angle_alpha 90.00 _cell.angle_alpha_esd ? _cell.angle_beta 90.00 _cell.angle_beta_esd ? _cell.angle_gamma 90.00 _cell.angle_gamma_esd ? _cell.entry_id 7F29 _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.00 _cell.length_a_esd ? _cell.length_b 1.00 _cell.length_b_esd ? _cell.length_c 1.00 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB ? _cell.reciprocal_angle_alpha ? _cell.reciprocal_angle_beta ? _cell.reciprocal_angle_gamma ? _cell.reciprocal_angle_alpha_esd ? _cell.reciprocal_angle_beta_esd ? _cell.reciprocal_angle_gamma_esd ? _cell.reciprocal_length_a ? _cell.reciprocal_length_b ? _cell.reciprocal_length_c ? _cell.reciprocal_length_a_esd ? _cell.reciprocal_length_b_esd ? _cell.reciprocal_length_c_esd ? _cell.pdbx_unique_axis ? _cell.pdbx_esd_method ? # _symmetry.entry_id 7F29 _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 ? # 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 'Amyloid-beta A4 protein' 3900.440 6 ? ? ? ? 2 branched syn 'beta-D-galactopyranose-(1-3)-2-amino-2-deoxy-alpha-D-galactopyranose' 341.312 6 ? ? ? ? 3 non-polymer syn 'ACETIC ACID' 60.052 6 ? ? ? ? # _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 HDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA _entity_poly.pdbx_seq_one_letter_code_can HDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA _entity_poly.pdbx_strand_id E,C,D,F,A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 HIS n 1 2 ASP n 1 3 SER n 1 4 GLY n 1 5 TYR n 1 6 GLU n 1 7 VAL n 1 8 HIS n 1 9 HIS n 1 10 GLN n 1 11 LYS n 1 12 LEU n 1 13 VAL n 1 14 PHE n 1 15 PHE n 1 16 ALA n 1 17 GLU n 1 18 ASP n 1 19 VAL n 1 20 GLY n 1 21 SER n 1 22 ASN n 1 23 LYS n 1 24 GLY n 1 25 ALA n 1 26 ILE n 1 27 ILE n 1 28 GLY n 1 29 LEU n 1 30 MET n 1 31 VAL n 1 32 GLY n 1 33 GLY n 1 34 VAL n 1 35 VAL n 1 36 ILE n 1 37 ALA 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 37 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code B4DM00_HUMAN _struct_ref.pdbx_db_accession B4DM00 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code HDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA _struct_ref.pdbx_align_begin 435 # 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 7F29 E 1 ? 37 ? B4DM00 435 ? 471 ? 6 42 2 1 7F29 C 1 ? 37 ? B4DM00 435 ? 471 ? 6 42 3 1 7F29 D 1 ? 37 ? B4DM00 435 ? 471 ? 6 42 4 1 7F29 F 1 ? 37 ? B4DM00 435 ? 471 ? 6 42 5 1 7F29 A 1 ? 37 ? B4DM00 435 ? 471 ? 6 42 6 1 7F29 B 1 ? 37 ? B4DM00 435 ? 471 ? 6 42 # 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 ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GAL 'D-saccharide, beta linking' . beta-D-galactopyranose 'beta-D-galactose; D-galactose; galactose' 'C6 H12 O6' 180.156 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 X6X 'D-saccharide, alpha linking' . 2-amino-2-deoxy-alpha-D-galactopyranose 'alpha-D-galactosamine; 2-amino-2-deoxy-alpha-D-galactose; 2-amino-2-deoxy-D-galactose; 2-amino-2-deoxy-galactose' 'C6 H13 N O5' 179.171 # _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 7F29 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _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 ? _refine.B_iso_mean ? _refine.B_iso_min ? _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 7F29 _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _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 . _refine.ls_d_res_low ? _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 ? _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs ? _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_R_factor_R_work ? _refine.ls_R_Fsqd_factor_obs ? _refine.ls_R_I_factor_obs ? _refine.ls_redundancy_reflns_all ? _refine.ls_redundancy_reflns_obs ? _refine.ls_restrained_S_all ? _refine.ls_restrained_S_obs ? _refine.ls_shift_over_esd_max ? _refine.ls_shift_over_esd_mean ? _refine.ls_structure_factor_coef ? _refine.ls_weighting_details ? _refine.ls_weighting_scheme ? _refine.ls_wR_factor_all ? _refine.ls_wR_factor_obs ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.solvent_model_details ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_R_complete ? _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 ? _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 ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_starting_model ? _refine.pdbx_stereochemistry_target_values 'GeoStd + Monomer Library + CDL v1.2' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_real_space_R ? _refine.pdbx_density_correlation ? _refine.pdbx_pd_number_of_powder_patterns ? _refine.pdbx_pd_number_of_points ? _refine.pdbx_pd_meas_number_of_points ? _refine.pdbx_pd_proc_ls_prof_R_factor ? _refine.pdbx_pd_proc_ls_prof_wR_factor ? _refine.pdbx_pd_Marquardt_correlation_coeff ? _refine.pdbx_pd_Fsqrd_R_factor ? _refine.pdbx_pd_ls_matrix_band_width ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_diffrn_id ? _refine.overall_SU_B ? _refine.overall_SU_ML ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_average_fsc_overall ? _refine.pdbx_average_fsc_work ? _refine.pdbx_average_fsc_free ? # 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 'ELECTRON MICROSCOPY' ? 0.0133 ? 1830 ? f_bond_d ? ? 'ELECTRON MICROSCOPY' ? 1.5598 ? 2472 ? f_angle_d ? ? 'ELECTRON MICROSCOPY' ? 0.0584 ? 306 ? f_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.0086 ? 294 ? f_plane_restr ? ? 'ELECTRON MICROSCOPY' ? 17.5294 ? 936 ? f_dihedral_angle_d ? ? # _struct.entry_id 7F29 _struct.title 'Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)' _struct.pdbx_structure_determination_methodology ? _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7F29 _struct_keywords.text 'amyloid fibril, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 1 ? D N N 1 ? E N N 1 ? F N N 1 ? G N N 2 ? H N N 2 ? I N N 2 ? J N N 2 ? K N N 2 ? L N N 2 ? M N N 3 ? N N N 3 ? O N N 3 ? P N N 3 ? Q N N 3 ? R N N 3 ? # 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 covale1 covale one ? M ACY . C ? ? ? 1_555 G X6X . N2 ? ? E ACY 101 G X6X 1 1_555 ? ? ? ? ? ? ? 1.456 ? ? covale2 covale one ? N ACY . C ? ? ? 1_555 H X6X . N2 ? ? C ACY 101 H X6X 1 1_555 ? ? ? ? ? ? ? 1.456 ? ? covale3 covale one ? O ACY . C ? ? ? 1_555 I X6X . N2 ? ? D ACY 101 I X6X 1 1_555 ? ? ? ? ? ? ? 1.456 ? ? covale4 covale one ? P ACY . C ? ? ? 1_555 J X6X . N2 ? ? F ACY 101 J X6X 1 1_555 ? ? ? ? ? ? ? 1.455 ? ? covale5 covale one ? Q ACY . C ? ? ? 1_555 K X6X . N2 ? ? A ACY 101 K X6X 1 1_555 ? ? ? ? ? ? ? 1.456 ? ? covale6 covale one ? R ACY . C ? ? ? 1_555 L X6X . N2 ? ? B ACY 101 L X6X 1 1_555 ? ? ? ? ? ? ? 1.455 ? ? covale7 covale both ? G X6X . O3 ? ? ? 1_555 G GAL . C1 ? ? G X6X 1 G GAL 2 1_555 ? ? ? ? ? ? ? 1.402 ? ? covale8 covale both ? H X6X . O3 ? ? ? 1_555 H GAL . C1 ? ? H X6X 1 H GAL 2 1_555 ? ? ? ? ? ? ? 1.402 ? ? covale9 covale both ? I X6X . O3 ? ? ? 1_555 I GAL . C1 ? ? I X6X 1 I GAL 2 1_555 ? ? ? ? ? ? ? 1.402 ? ? covale10 covale both ? J X6X . O3 ? ? ? 1_555 J GAL . C1 ? ? J X6X 1 J GAL 2 1_555 ? ? ? ? ? ? ? 1.402 ? ? covale11 covale both ? K X6X . O3 ? ? ? 1_555 K GAL . C1 ? ? K X6X 1 K GAL 2 1_555 ? ? ? ? ? ? ? 1.403 ? ? covale12 covale both ? L X6X . O3 ? ? ? 1_555 L GAL . C1 ? ? L X6X 1 L GAL 2 1_555 ? ? ? ? ? ? ? 1.403 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 3 ? AA2 ? 3 ? AA3 ? 3 ? AA4 ? 3 ? AA5 ? 3 ? AA6 ? 3 ? AA7 ? 3 ? AA8 ? 3 ? # 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 ? parallel AA1 2 3 ? parallel AA2 1 2 ? parallel AA2 2 3 ? parallel AA3 1 2 ? parallel AA3 2 3 ? parallel AA4 1 2 ? parallel AA4 2 3 ? parallel AA5 1 2 ? parallel AA5 2 3 ? parallel AA6 1 2 ? parallel AA6 2 3 ? parallel AA7 1 2 ? parallel AA7 2 3 ? parallel AA8 1 2 ? parallel AA8 2 3 ? 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 GLU B 6 ? VAL B 7 ? GLU C 11 VAL C 12 AA1 2 GLU A 6 ? VAL A 7 ? GLU E 11 VAL E 12 AA1 3 GLU C 6 ? VAL C 7 ? GLU D 11 VAL D 12 AA2 1 GLN B 10 ? ASN B 22 ? GLN C 15 ASN C 27 AA2 2 GLN A 10 ? ASN A 22 ? GLN E 15 ASN E 27 AA2 3 GLN C 10 ? ASN C 22 ? GLN D 15 ASN D 27 AA3 1 ALA B 25 ? MET B 30 ? ALA C 30 MET C 35 AA3 2 ALA A 25 ? MET A 30 ? ALA E 30 MET E 35 AA3 3 ALA C 25 ? MET C 30 ? ALA D 30 MET D 35 AA4 1 VAL B 34 ? ILE B 36 ? VAL C 39 ILE C 41 AA4 2 VAL A 34 ? ILE A 36 ? VAL E 39 ILE E 41 AA4 3 VAL C 34 ? ILE C 36 ? VAL D 39 ILE D 41 AA5 1 GLU E 6 ? VAL E 7 ? GLU A 11 VAL A 12 AA5 2 GLU D 6 ? VAL D 7 ? GLU F 11 VAL F 12 AA5 3 GLU F 6 ? VAL F 7 ? GLU B 11 VAL B 12 AA6 1 GLN E 10 ? ASN E 22 ? GLN A 15 ASN A 27 AA6 2 GLN D 10 ? ASN D 22 ? GLN F 15 ASN F 27 AA6 3 GLN F 10 ? ASN F 22 ? GLN B 15 ASN B 27 AA7 1 ALA E 25 ? MET E 30 ? ALA A 30 MET A 35 AA7 2 ALA D 25 ? MET D 30 ? ALA F 30 MET F 35 AA7 3 ALA F 25 ? MET F 30 ? ALA B 30 MET B 35 AA8 1 VAL E 34 ? ILE E 36 ? VAL A 39 ILE A 41 AA8 2 VAL D 34 ? ILE D 36 ? VAL F 39 ILE F 41 AA8 3 VAL F 34 ? ILE F 36 ? VAL B 39 ILE B 41 # 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 O VAL B 7 ? O VAL C 12 N GLU A 6 ? N GLU E 11 AA1 2 3 N VAL A 7 ? N VAL E 12 O GLU C 6 ? O GLU D 11 AA2 1 2 O GLU B 17 ? O GLU C 22 N ASP A 18 ? N ASP E 23 AA2 2 3 N GLU A 17 ? N GLU E 22 O ASP C 18 ? O ASP D 23 AA3 1 2 O LEU B 29 ? O LEU C 34 N MET A 30 ? N MET E 35 AA3 2 3 N LEU A 29 ? N LEU E 34 O MET C 30 ? O MET D 35 AA4 1 2 O ILE B 36 ? O ILE C 41 N VAL A 35 ? N VAL E 40 AA4 2 3 N ILE A 36 ? N ILE E 41 O VAL C 35 ? O VAL D 40 AA5 1 2 O VAL E 7 ? O VAL A 12 N GLU D 6 ? N GLU F 11 AA5 2 3 N VAL D 7 ? N VAL F 12 O GLU F 6 ? O GLU B 11 AA6 1 2 O GLU E 17 ? O GLU A 22 N ASP D 18 ? N ASP F 23 AA6 2 3 N GLU D 17 ? N GLU F 22 O ASP F 18 ? O ASP B 23 AA7 1 2 O LEU E 29 ? O LEU A 34 N MET D 30 ? N MET F 35 AA7 2 3 N LEU D 29 ? N LEU F 34 O MET F 30 ? O MET B 35 AA8 1 2 O ILE E 36 ? O ILE A 41 N VAL D 35 ? N VAL F 40 AA8 2 3 N ILE D 36 ? N ILE F 41 O VAL F 35 ? O VAL B 40 # _atom_sites.entry_id 7F29 _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C N O S # 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 HIS 1 6 6 HIS HIS E . n A 1 2 ASP 2 7 7 ASP ASP E . n A 1 3 SER 3 8 8 SER SER E . n A 1 4 GLY 4 9 9 GLY GLY E . n A 1 5 TYR 5 10 10 TYR TYR E . n A 1 6 GLU 6 11 11 GLU GLU E . n A 1 7 VAL 7 12 12 VAL VAL E . n A 1 8 HIS 8 13 13 HIS HIS E . n A 1 9 HIS 9 14 14 HIS HIS E . n A 1 10 GLN 10 15 15 GLN GLN E . n A 1 11 LYS 11 16 16 LYS LYS E . n A 1 12 LEU 12 17 17 LEU LEU E . n A 1 13 VAL 13 18 18 VAL VAL E . n A 1 14 PHE 14 19 19 PHE PHE E . n A 1 15 PHE 15 20 20 PHE PHE E . n A 1 16 ALA 16 21 21 ALA ALA E . n A 1 17 GLU 17 22 22 GLU GLU E . n A 1 18 ASP 18 23 23 ASP ASP E . n A 1 19 VAL 19 24 24 VAL VAL E . n A 1 20 GLY 20 25 25 GLY GLY E . n A 1 21 SER 21 26 26 SER SER E . n A 1 22 ASN 22 27 27 ASN ASN E . n A 1 23 LYS 23 28 28 LYS LYS E . n A 1 24 GLY 24 29 29 GLY GLY E . n A 1 25 ALA 25 30 30 ALA ALA E . n A 1 26 ILE 26 31 31 ILE ILE E . n A 1 27 ILE 27 32 32 ILE ILE E . n A 1 28 GLY 28 33 33 GLY GLY E . n A 1 29 LEU 29 34 34 LEU LEU E . n A 1 30 MET 30 35 35 MET MET E . n A 1 31 VAL 31 36 36 VAL VAL E . n A 1 32 GLY 32 37 37 GLY GLY E . n A 1 33 GLY 33 38 38 GLY GLY E . n A 1 34 VAL 34 39 39 VAL VAL E . n A 1 35 VAL 35 40 40 VAL VAL E . n A 1 36 ILE 36 41 41 ILE ILE E . n A 1 37 ALA 37 42 42 ALA ALA E . n B 1 1 HIS 1 6 6 HIS HIS C . n B 1 2 ASP 2 7 7 ASP ASP C . n B 1 3 SER 3 8 8 SER SER C . n B 1 4 GLY 4 9 9 GLY GLY C . n B 1 5 TYR 5 10 10 TYR TYR C . n B 1 6 GLU 6 11 11 GLU GLU C . n B 1 7 VAL 7 12 12 VAL VAL C . n B 1 8 HIS 8 13 13 HIS HIS C . n B 1 9 HIS 9 14 14 HIS HIS C . n B 1 10 GLN 10 15 15 GLN GLN C . n B 1 11 LYS 11 16 16 LYS LYS C . n B 1 12 LEU 12 17 17 LEU LEU C . n B 1 13 VAL 13 18 18 VAL VAL C . n B 1 14 PHE 14 19 19 PHE PHE C . n B 1 15 PHE 15 20 20 PHE PHE C . n B 1 16 ALA 16 21 21 ALA ALA C . n B 1 17 GLU 17 22 22 GLU GLU C . n B 1 18 ASP 18 23 23 ASP ASP C . n B 1 19 VAL 19 24 24 VAL VAL C . n B 1 20 GLY 20 25 25 GLY GLY C . n B 1 21 SER 21 26 26 SER SER C . n B 1 22 ASN 22 27 27 ASN ASN C . n B 1 23 LYS 23 28 28 LYS LYS C . n B 1 24 GLY 24 29 29 GLY GLY C . n B 1 25 ALA 25 30 30 ALA ALA C . n B 1 26 ILE 26 31 31 ILE ILE C . n B 1 27 ILE 27 32 32 ILE ILE C . n B 1 28 GLY 28 33 33 GLY GLY C . n B 1 29 LEU 29 34 34 LEU LEU C . n B 1 30 MET 30 35 35 MET MET C . n B 1 31 VAL 31 36 36 VAL VAL C . n B 1 32 GLY 32 37 37 GLY GLY C . n B 1 33 GLY 33 38 38 GLY GLY C . n B 1 34 VAL 34 39 39 VAL VAL C . n B 1 35 VAL 35 40 40 VAL VAL C . n B 1 36 ILE 36 41 41 ILE ILE C . n B 1 37 ALA 37 42 42 ALA ALA C . n C 1 1 HIS 1 6 6 HIS HIS D . n C 1 2 ASP 2 7 7 ASP ASP D . n C 1 3 SER 3 8 8 SER SER D . n C 1 4 GLY 4 9 9 GLY GLY D . n C 1 5 TYR 5 10 10 TYR TYR D . n C 1 6 GLU 6 11 11 GLU GLU D . n C 1 7 VAL 7 12 12 VAL VAL D . n C 1 8 HIS 8 13 13 HIS HIS D . n C 1 9 HIS 9 14 14 HIS HIS D . n C 1 10 GLN 10 15 15 GLN GLN D . n C 1 11 LYS 11 16 16 LYS LYS D . n C 1 12 LEU 12 17 17 LEU LEU D . n C 1 13 VAL 13 18 18 VAL VAL D . n C 1 14 PHE 14 19 19 PHE PHE D . n C 1 15 PHE 15 20 20 PHE PHE D . n C 1 16 ALA 16 21 21 ALA ALA D . n C 1 17 GLU 17 22 22 GLU GLU D . n C 1 18 ASP 18 23 23 ASP ASP D . n C 1 19 VAL 19 24 24 VAL VAL D . n C 1 20 GLY 20 25 25 GLY GLY D . n C 1 21 SER 21 26 26 SER SER D . n C 1 22 ASN 22 27 27 ASN ASN D . n C 1 23 LYS 23 28 28 LYS LYS D . n C 1 24 GLY 24 29 29 GLY GLY D . n C 1 25 ALA 25 30 30 ALA ALA D . n C 1 26 ILE 26 31 31 ILE ILE D . n C 1 27 ILE 27 32 32 ILE ILE D . n C 1 28 GLY 28 33 33 GLY GLY D . n C 1 29 LEU 29 34 34 LEU LEU D . n C 1 30 MET 30 35 35 MET MET D . n C 1 31 VAL 31 36 36 VAL VAL D . n C 1 32 GLY 32 37 37 GLY GLY D . n C 1 33 GLY 33 38 38 GLY GLY D . n C 1 34 VAL 34 39 39 VAL VAL D . n C 1 35 VAL 35 40 40 VAL VAL D . n C 1 36 ILE 36 41 41 ILE ILE D . n C 1 37 ALA 37 42 42 ALA ALA D . n D 1 1 HIS 1 6 6 HIS HIS F . n D 1 2 ASP 2 7 7 ASP ASP F . n D 1 3 SER 3 8 8 SER SER F . n D 1 4 GLY 4 9 9 GLY GLY F . n D 1 5 TYR 5 10 10 TYR TYR F . n D 1 6 GLU 6 11 11 GLU GLU F . n D 1 7 VAL 7 12 12 VAL VAL F . n D 1 8 HIS 8 13 13 HIS HIS F . n D 1 9 HIS 9 14 14 HIS HIS F . n D 1 10 GLN 10 15 15 GLN GLN F . n D 1 11 LYS 11 16 16 LYS LYS F . n D 1 12 LEU 12 17 17 LEU LEU F . n D 1 13 VAL 13 18 18 VAL VAL F . n D 1 14 PHE 14 19 19 PHE PHE F . n D 1 15 PHE 15 20 20 PHE PHE F . n D 1 16 ALA 16 21 21 ALA ALA F . n D 1 17 GLU 17 22 22 GLU GLU F . n D 1 18 ASP 18 23 23 ASP ASP F . n D 1 19 VAL 19 24 24 VAL VAL F . n D 1 20 GLY 20 25 25 GLY GLY F . n D 1 21 SER 21 26 26 SER SER F . n D 1 22 ASN 22 27 27 ASN ASN F . n D 1 23 LYS 23 28 28 LYS LYS F . n D 1 24 GLY 24 29 29 GLY GLY F . n D 1 25 ALA 25 30 30 ALA ALA F . n D 1 26 ILE 26 31 31 ILE ILE F . n D 1 27 ILE 27 32 32 ILE ILE F . n D 1 28 GLY 28 33 33 GLY GLY F . n D 1 29 LEU 29 34 34 LEU LEU F . n D 1 30 MET 30 35 35 MET MET F . n D 1 31 VAL 31 36 36 VAL VAL F . n D 1 32 GLY 32 37 37 GLY GLY F . n D 1 33 GLY 33 38 38 GLY GLY F . n D 1 34 VAL 34 39 39 VAL VAL F . n D 1 35 VAL 35 40 40 VAL VAL F . n D 1 36 ILE 36 41 41 ILE ILE F . n D 1 37 ALA 37 42 42 ALA ALA F . n E 1 1 HIS 1 6 6 HIS HIS A . n E 1 2 ASP 2 7 7 ASP ASP A . n E 1 3 SER 3 8 8 SER SER A . n E 1 4 GLY 4 9 9 GLY GLY A . n E 1 5 TYR 5 10 10 TYR TYR A . n E 1 6 GLU 6 11 11 GLU GLU A . n E 1 7 VAL 7 12 12 VAL VAL A . n E 1 8 HIS 8 13 13 HIS HIS A . n E 1 9 HIS 9 14 14 HIS HIS A . n E 1 10 GLN 10 15 15 GLN GLN A . n E 1 11 LYS 11 16 16 LYS LYS A . n E 1 12 LEU 12 17 17 LEU LEU A . n E 1 13 VAL 13 18 18 VAL VAL A . n E 1 14 PHE 14 19 19 PHE PHE A . n E 1 15 PHE 15 20 20 PHE PHE A . n E 1 16 ALA 16 21 21 ALA ALA A . n E 1 17 GLU 17 22 22 GLU GLU A . n E 1 18 ASP 18 23 23 ASP ASP A . n E 1 19 VAL 19 24 24 VAL VAL A . n E 1 20 GLY 20 25 25 GLY GLY A . n E 1 21 SER 21 26 26 SER SER A . n E 1 22 ASN 22 27 27 ASN ASN A . n E 1 23 LYS 23 28 28 LYS LYS A . n E 1 24 GLY 24 29 29 GLY GLY A . n E 1 25 ALA 25 30 30 ALA ALA A . n E 1 26 ILE 26 31 31 ILE ILE A . n E 1 27 ILE 27 32 32 ILE ILE A . n E 1 28 GLY 28 33 33 GLY GLY A . n E 1 29 LEU 29 34 34 LEU LEU A . n E 1 30 MET 30 35 35 MET MET A . n E 1 31 VAL 31 36 36 VAL VAL A . n E 1 32 GLY 32 37 37 GLY GLY A . n E 1 33 GLY 33 38 38 GLY GLY A . n E 1 34 VAL 34 39 39 VAL VAL A . n E 1 35 VAL 35 40 40 VAL VAL A . n E 1 36 ILE 36 41 41 ILE ILE A . n E 1 37 ALA 37 42 42 ALA ALA A . n F 1 1 HIS 1 6 6 HIS HIS B . n F 1 2 ASP 2 7 7 ASP ASP B . n F 1 3 SER 3 8 8 SER SER B . n F 1 4 GLY 4 9 9 GLY GLY B . n F 1 5 TYR 5 10 10 TYR TYR B . n F 1 6 GLU 6 11 11 GLU GLU B . n F 1 7 VAL 7 12 12 VAL VAL B . n F 1 8 HIS 8 13 13 HIS HIS B . n F 1 9 HIS 9 14 14 HIS HIS B . n F 1 10 GLN 10 15 15 GLN GLN B . n F 1 11 LYS 11 16 16 LYS LYS B . n F 1 12 LEU 12 17 17 LEU LEU B . n F 1 13 VAL 13 18 18 VAL VAL B . n F 1 14 PHE 14 19 19 PHE PHE B . n F 1 15 PHE 15 20 20 PHE PHE B . n F 1 16 ALA 16 21 21 ALA ALA B . n F 1 17 GLU 17 22 22 GLU GLU B . n F 1 18 ASP 18 23 23 ASP ASP B . n F 1 19 VAL 19 24 24 VAL VAL B . n F 1 20 GLY 20 25 25 GLY GLY B . n F 1 21 SER 21 26 26 SER SER B . n F 1 22 ASN 22 27 27 ASN ASN B . n F 1 23 LYS 23 28 28 LYS LYS B . n F 1 24 GLY 24 29 29 GLY GLY B . n F 1 25 ALA 25 30 30 ALA ALA B . n F 1 26 ILE 26 31 31 ILE ILE B . n F 1 27 ILE 27 32 32 ILE ILE B . n F 1 28 GLY 28 33 33 GLY GLY B . n F 1 29 LEU 29 34 34 LEU LEU B . n F 1 30 MET 30 35 35 MET MET B . n F 1 31 VAL 31 36 36 VAL VAL B . n F 1 32 GLY 32 37 37 GLY GLY B . n F 1 33 GLY 33 38 38 GLY GLY B . n F 1 34 VAL 34 39 39 VAL VAL B . n F 1 35 VAL 35 40 40 VAL VAL B . n F 1 36 ILE 36 41 41 ILE ILE B . n F 1 37 ALA 37 42 42 ALA ALA B . n # _pdbx_contact_author.id 2 _pdbx_contact_author.email xiawc@sioc.ac.cn _pdbx_contact_author.name_first Cong _pdbx_contact_author.name_last Liu _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0003-3425-6672 # 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 M 3 ACY 1 101 1 ACY GBG E . N 3 ACY 1 101 1 ACY GBG C . O 3 ACY 1 101 1 ACY GBG D . P 3 ACY 1 101 1 ACY GBG F . Q 3 ACY 1 101 1 ACY GBG A . R 3 ACY 1 101 1 ACY GBG B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R # _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 ? _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 # _pdbx_audit_revision_history.ordinal 1 _pdbx_audit_revision_history.data_content_type 'Structure model' _pdbx_audit_revision_history.major_revision 1 _pdbx_audit_revision_history.minor_revision 0 _pdbx_audit_revision_history.revision_date 2022-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _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 ? ? 'Paul D. Adams' pdadams@lbl.gov ? ? ? ? Python/C++ https://www.phenix-online.org/ ? phenix.real_space_refine ? ? program 1.15.2_3472 1 ? refinement ? ? 'Paul D. Adams' pdadams@lbl.gov ? ? ? ? Python/C++ https://www.phenix-online.org/ ? PHENIX ? ? program 1.15.2_3472 2 # _pdbx_entry_details.entry_id 7F29 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N # _em_3d_fitting.entry_id 7F29 _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol ? _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 7F29 _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 92523 _em_3d_reconstruction.resolution 3.1 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type HELICAL _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.magnification_calibration ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 4.0 _em_buffer.specimen_id 1 _em_buffer.name ? # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.details ? _em_entity_assembly.name 'Cryo-EM structure of the fibril formed by disaccharide-modified amyloid-beta(1-42)' _em_entity_assembly.source SYNTHETIC _em_entity_assembly.type 'ORGANELLE OR CELLULAR COMPONENT' _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 7F29 _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TITAN KRIOS' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max 2000 _em_imaging.nominal_defocus_min 1000 _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _em_imaging.specimen_id 1 _em_imaging.citation_id ? _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.specimen_holder_type ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.entry_id 7F29 _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 7F29 _em_experiment.id 1 _em_experiment.aggregation_state FILAMENT _em_experiment.reconstruction_method HELICAL _em_experiment.entity_assembly_id 1 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 CZ F TYR 10 ? ? O1 J X6X 1 ? ? 1.37 2 1 CZ A TYR 10 ? ? O1 K X6X 1 ? ? 1.37 3 1 CZ E TYR 10 ? ? O1 G X6X 1 ? ? 1.37 4 1 CZ D TYR 10 ? ? O1 I X6X 1 ? ? 1.37 5 1 CZ B TYR 10 ? ? O1 L X6X 1 ? ? 1.37 6 1 CZ C TYR 10 ? ? O1 H X6X 1 ? ? 1.37 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 GLU E 22 ? ? -93.87 -61.78 2 1 GLU C 22 ? ? -93.91 -61.74 3 1 GLU D 22 ? ? -93.87 -61.74 4 1 GLU F 22 ? ? -93.90 -61.76 5 1 GLU A 22 ? ? -93.88 -61.80 6 1 GLU B 22 ? ? -93.88 -61.81 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 E TYR 10 ? OH ? A TYR 5 OH 2 1 Y 1 C TYR 10 ? OH ? B TYR 5 OH 3 1 Y 1 D TYR 10 ? OH ? C TYR 5 OH 4 1 Y 1 F TYR 10 ? OH ? D TYR 5 OH 5 1 Y 1 A TYR 10 ? OH ? E TYR 5 OH 6 1 Y 1 B TYR 10 ? OH ? F TYR 5 OH # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type NONE _em_ctf_correction.details ? # _em_entity_assembly_naturalsource.id 1 _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.ncbi_tax_id 9606 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Homo sapiens' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_synthetic.cell ? _em_entity_assembly_synthetic.cellular_location ? _em_entity_assembly_synthetic.entity_assembly_id 1 _em_entity_assembly_synthetic.id 1 _em_entity_assembly_synthetic.ncbi_tax_id 9606 _em_entity_assembly_synthetic.organ ? _em_entity_assembly_synthetic.organelle ? _em_entity_assembly_synthetic.organism 'Homo sapiens' _em_entity_assembly_synthetic.strain ? _em_entity_assembly_synthetic.tissue ? # _em_helical_entity.id 1 _em_helical_entity.image_processing_id 1 _em_helical_entity.angular_rotation_per_subunit 179.324 _em_helical_entity.axial_rise_per_subunit 2.40 _em_helical_entity.axial_symmetry C1 _em_helical_entity.details ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.avg_electron_dose_per_image 55 _em_image_recording.average_exposure_time ? _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? _em_image_recording.avg_electron_dose_per_subtomogram ? # loop_ _em_software.id _em_software.category _em_software.details _em_software.name _em_software.version _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id 1 'PARTICLE SELECTION' ? ? ? 1 ? ? 2 'IMAGE ACQUISITION' ? ? ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? ? ? 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? ? ? ? ? ? 8 'MODEL REFINEMENT' ? ? ? ? ? ? 9 OTHER ? ? ? ? ? ? 10 'INITIAL EULER ASSIGNMENT' ? ? ? 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? ? ? 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? ? ? 1 ? ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # _pdbx_audit_support.funding_organization 'Not funded' _pdbx_audit_support.country ? _pdbx_audit_support.grant_number ? _pdbx_audit_support.ordinal 1 # loop_ _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_mon_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.hetero G 2 X6X 1 G X6X 1 E GBG 1 n G 2 GAL 2 G GAL 2 E GBG 1 n H 2 X6X 1 H X6X 1 C GBG 1 n H 2 GAL 2 H GAL 2 C GBG 1 n I 2 X6X 1 I X6X 1 D GBG 1 n I 2 GAL 2 I GAL 2 D GBG 1 n J 2 X6X 1 J X6X 1 F GBG 1 n J 2 GAL 2 J GAL 2 F GBG 1 n K 2 X6X 1 K X6X 1 A GBG 1 n K 2 GAL 2 K GAL 2 A GBG 1 n L 2 X6X 1 L X6X 1 B GBG 1 n L 2 GAL 2 L GAL 2 B GBG 1 n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier GAL 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGalpb GAL 'COMMON NAME' GMML 1.0 b-D-galactopyranose GAL 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 b-D-Galp GAL 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Gal X6X 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DGalpNa X6X 'COMMON NAME' GMML 1.0 a-D-galactopyranosamine X6X 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-GalpN X6X 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 GalN # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_descriptor.ordinal _pdbx_entity_branch_descriptor.entity_id _pdbx_entity_branch_descriptor.descriptor _pdbx_entity_branch_descriptor.type _pdbx_entity_branch_descriptor.program _pdbx_entity_branch_descriptor.program_version 1 2 DGalpb1-3DGalpNa1-ROH 'Glycam Condensed Sequence' GMML 1.0 2 2 'WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*N][a2112h-1b_1-5]/1-2/a3-b1' WURCS PDB2Glycan 1.1.0 3 2 '[][a-D-GalpN]{[(3+1)][b-D-Galp]{}}' LINUCS PDB-CARE ? # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.comp_id_1 GAL _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_2 X6X _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.value_order sing _pdbx_entity_branch_link.details ? # loop_ _pdbx_entity_branch_list.entity_id _pdbx_entity_branch_list.comp_id _pdbx_entity_branch_list.num _pdbx_entity_branch_list.hetero 2 X6X 1 n 2 GAL 2 n # _pdbx_entity_nonpoly.entity_id 3 _pdbx_entity_nonpoly.name 'ACETIC ACID' _pdbx_entity_nonpoly.comp_id ACY # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? #