data_8J5A # _entry.id 8J5A # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.373 _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 8J5A pdb_00008j5a 10.2210/pdb8j5a/pdb WWPDB D_1300037218 ? ? EMDB EMD-35984 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type EMDB . EMD-35981 'other EM volume' EMDB 'Structure of apoferritin from Mus musculus by cryo-electron microscopy' EMD-35984 '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 8J5A _pdbx_database_status.recvd_initial_deposition_date 2023-04-21 _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 'Kawakami, K.' 1 0000-0002-1689-1819 'Maki-Yonekura, S.' 2 0000-0002-8295-8794 'Hamaguchi, T.' 3 0000-0003-0876-7700 'Takaba, K.' 4 0000-0002-2927-0608 'Yonekura, K.' 5 0000-0001-5520-4391 # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Commun Chem' _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2399-3669 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 6 _citation.language ? _citation.page_first 98 _citation.page_last 98 _citation.title 'Measurement of charges and chemical bonding in a cryo-EM structure.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1038/s42004-023-00900-x _citation.pdbx_database_id_PubMed 37258702 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Maki-Yonekura, S.' 1 0000-0002-8295-8794 primary 'Kawakami, K.' 2 0000-0002-1689-1819 primary 'Takaba, K.' 3 0000-0002-2927-0608 primary 'Hamaguchi, T.' 4 ? primary 'Yonekura, K.' 5 0000-0001-5520-4391 # _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 8J5A _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 8J5A _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 man 'Ferritin heavy chain' 20079.594 1 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 1 ? ? ? ? 3 water nat water 18.015 141 ? ? ? ? # _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 ;PSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQD IKKPDRDDWESGLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAG MAEYLFDKHTLG ; _entity_poly.pdbx_seq_one_letter_code_can ;PSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQD IKKPDRDDWESGLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAG MAEYLFDKHTLG ; _entity_poly.pdbx_strand_id A _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 PRO n 1 2 SER n 1 3 GLN n 1 4 VAL n 1 5 ARG n 1 6 GLN n 1 7 ASN n 1 8 TYR n 1 9 HIS n 1 10 GLN n 1 11 ASP n 1 12 ALA n 1 13 GLU n 1 14 ALA n 1 15 ALA n 1 16 ILE n 1 17 ASN n 1 18 ARG n 1 19 GLN n 1 20 ILE n 1 21 ASN n 1 22 LEU n 1 23 GLU n 1 24 LEU n 1 25 TYR n 1 26 ALA n 1 27 SER n 1 28 TYR n 1 29 VAL n 1 30 TYR n 1 31 LEU n 1 32 SER n 1 33 MET n 1 34 SER n 1 35 CYS n 1 36 TYR n 1 37 PHE n 1 38 ASP n 1 39 ARG n 1 40 ASP n 1 41 ASP n 1 42 VAL n 1 43 ALA n 1 44 LEU n 1 45 LYS n 1 46 ASN n 1 47 PHE n 1 48 ALA n 1 49 LYS n 1 50 TYR n 1 51 PHE n 1 52 LEU n 1 53 HIS n 1 54 GLN n 1 55 SER n 1 56 HIS n 1 57 GLU n 1 58 GLU n 1 59 ARG n 1 60 GLU n 1 61 HIS n 1 62 ALA n 1 63 GLU n 1 64 LYS n 1 65 LEU n 1 66 MET n 1 67 LYS n 1 68 LEU n 1 69 GLN n 1 70 ASN n 1 71 GLN n 1 72 ARG n 1 73 GLY n 1 74 GLY n 1 75 ARG n 1 76 ILE n 1 77 PHE n 1 78 LEU n 1 79 GLN n 1 80 ASP n 1 81 ILE n 1 82 LYS n 1 83 LYS n 1 84 PRO n 1 85 ASP n 1 86 ARG n 1 87 ASP n 1 88 ASP n 1 89 TRP n 1 90 GLU n 1 91 SER n 1 92 GLY n 1 93 LEU n 1 94 ASN n 1 95 ALA n 1 96 MET n 1 97 GLU n 1 98 CYS n 1 99 ALA n 1 100 LEU n 1 101 HIS n 1 102 LEU n 1 103 GLU n 1 104 LYS n 1 105 SER n 1 106 VAL n 1 107 ASN n 1 108 GLN n 1 109 SER n 1 110 LEU n 1 111 LEU n 1 112 GLU n 1 113 LEU n 1 114 HIS n 1 115 LYS n 1 116 LEU n 1 117 ALA n 1 118 THR n 1 119 ASP n 1 120 LYS n 1 121 ASN n 1 122 ASP n 1 123 PRO n 1 124 HIS n 1 125 LEU n 1 126 CYS n 1 127 ASP n 1 128 PHE n 1 129 ILE n 1 130 GLU n 1 131 THR n 1 132 TYR n 1 133 TYR n 1 134 LEU n 1 135 SER n 1 136 GLU n 1 137 GLN n 1 138 VAL n 1 139 LYS n 1 140 SER n 1 141 ILE n 1 142 LYS n 1 143 GLU n 1 144 LEU n 1 145 GLY n 1 146 ASP n 1 147 HIS n 1 148 VAL n 1 149 THR n 1 150 ASN n 1 151 LEU n 1 152 ARG n 1 153 LYS n 1 154 MET n 1 155 GLY n 1 156 ALA n 1 157 PRO n 1 158 GLU n 1 159 ALA n 1 160 GLY n 1 161 MET n 1 162 ALA n 1 163 GLU n 1 164 TYR n 1 165 LEU n 1 166 PHE n 1 167 ASP n 1 168 LYS n 1 169 HIS n 1 170 THR n 1 171 LEU n 1 172 GLY n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 172 _entity_src_gen.gene_src_common_name 'house mouse' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'Fth1, Fth' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code FRIH_MOUSE _struct_ref.pdbx_db_accession P09528 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;PSQVRQNYHQDAEAAINRQINLELYASYVYLSMSCYFDRDDVALKNFAKYFLHQSHEEREHAEKLMKLQNQRGGRIFLQD IKKPDRDDWESGLNAMECALHLEKSVNQSLLELHKLATDKNDPHLCDFIETYYLSEQVKSIKELGDHVTNLRKMGAPEAG MAEYLFDKHTLG ; _struct_ref.pdbx_align_begin 6 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8J5A _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 172 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P09528 _struct_ref_seq.db_align_beg 6 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 177 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 5 _struct_ref_seq.pdbx_auth_seq_align_end 176 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 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 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 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 HOH non-polymer . WATER ? 'H2 O' 18.015 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _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 8J5A _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 15.683 _refine.B_iso_min ? _refine.correlation_coeff_Fo_to_Fc 0.801 _refine.correlation_coeff_Fo_to_Fc_free ? _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.diff_density_max ? _refine.diff_density_max_esd ? _refine.diff_density_min ? _refine.diff_density_min_esd ? _refine.diff_density_rms ? _refine.diff_density_rms_esd ? _refine.entry_id 8J5A _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 1.19 _refine.ls_d_res_low 126.72 _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 2529386 _refine.ls_number_reflns_R_free ? _refine.ls_number_reflns_R_work ? _refine.ls_number_restraints ? _refine.ls_percent_reflns_obs 100.00 _refine.ls_percent_reflns_R_free ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.24069 _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 0.24069 _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 'PARAMETERS FOR MASK CACLULATION' _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 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_overall_ESU_R 0.007 _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 0.528 _refine.overall_SU_ML 0.022 _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 ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id 1 _refine_hist.details ? _refine_hist.d_res_high . _refine_hist.d_res_low . _refine_hist.number_atoms_solvent ? _refine_hist.number_atoms_total 1632 _refine_hist.number_reflns_all ? _refine_hist.number_reflns_obs ? _refine_hist.number_reflns_R_free ? _refine_hist.number_reflns_R_work ? _refine_hist.R_factor_all ? _refine_hist.R_factor_obs ? _refine_hist.R_factor_R_free ? _refine_hist.R_factor_R_work ? _refine_hist.pdbx_number_residues_total ? _refine_hist.pdbx_B_iso_mean_ligand ? _refine_hist.pdbx_B_iso_mean_solvent ? _refine_hist.pdbx_number_atoms_protein ? _refine_hist.pdbx_number_atoms_nucleic_acid ? _refine_hist.pdbx_number_atoms_ligand ? _refine_hist.pdbx_number_atoms_lipid ? _refine_hist.pdbx_number_atoms_carb ? _refine_hist.pdbx_pseudo_atom_details ? # loop_ _refine_ls_restr.pdbx_refine_id _refine_ls_restr.criterion _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.number _refine_ls_restr.rejects _refine_ls_restr.type _refine_ls_restr.weight _refine_ls_restr.pdbx_restraint_function 'ELECTRON MICROSCOPY' ? 0.017 0.013 1542 ? r_bond_refined_d ? ? 'ELECTRON MICROSCOPY' ? 0.011 0.015 1381 ? r_bond_other_d ? ? 'ELECTRON MICROSCOPY' ? 1.495 1.632 2123 ? r_angle_refined_deg ? ? 'ELECTRON MICROSCOPY' ? 1.860 1.578 3187 ? r_angle_other_deg ? ? 'ELECTRON MICROSCOPY' ? 4.722 5.000 214 ? r_dihedral_angle_1_deg ? ? 'ELECTRON MICROSCOPY' ? 38.116 23.049 82 ? r_dihedral_angle_2_deg ? ? 'ELECTRON MICROSCOPY' ? 13.288 15.000 254 ? r_dihedral_angle_3_deg ? ? 'ELECTRON MICROSCOPY' ? 19.938 15.000 7 ? r_dihedral_angle_4_deg ? ? 'ELECTRON MICROSCOPY' ? 0.077 0.200 200 ? r_chiral_restr ? ? 'ELECTRON MICROSCOPY' ? 0.007 0.020 1875 ? r_gen_planes_refined ? ? 'ELECTRON MICROSCOPY' ? 0.003 0.020 379 ? r_gen_planes_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_nbtor_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_xyhbond_nbd_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_vdw_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_hbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_refined ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_symmetry_metal_ion_other ? ? 'ELECTRON MICROSCOPY' ? 0.823 1.523 769 ? r_mcbond_it ? ? 'ELECTRON MICROSCOPY' ? 0.802 1.520 767 ? r_mcbond_other ? ? 'ELECTRON MICROSCOPY' ? 1.351 2.286 984 ? r_mcangle_it ? ? 'ELECTRON MICROSCOPY' ? 1.338 2.285 984 ? r_mcangle_other ? ? 'ELECTRON MICROSCOPY' ? 1.564 1.757 773 ? r_scbond_it ? ? 'ELECTRON MICROSCOPY' ? 1.563 1.758 774 ? r_scbond_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_scangle_it ? ? 'ELECTRON MICROSCOPY' ? 2.553 2.559 1129 ? r_scangle_other ? ? 'ELECTRON MICROSCOPY' ? 6.105 33.862 8721 ? r_long_range_B_refined ? ? 'ELECTRON MICROSCOPY' ? 6.049 33.221 8598 ? r_long_range_B_other ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_rigid_bond_restr ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_free ? ? 'ELECTRON MICROSCOPY' ? ? ? ? ? r_sphericity_bonded ? ? # _refine_ls_shell.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_ls_shell.d_res_high 1.190 _refine_ls_shell.d_res_low 1.221 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.number_reflns_R_free 0 _refine_ls_shell.number_reflns_R_work 187647 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_obs ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.R_factor_R_work ? _refine_ls_shell.redundancy_reflns_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.wR_factor_all ? _refine_ls_shell.wR_factor_obs ? _refine_ls_shell.wR_factor_R_free ? _refine_ls_shell.wR_factor_R_work ? _refine_ls_shell.pdbx_R_complete ? _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.pdbx_phase_error ? _refine_ls_shell.pdbx_fsc_work ? _refine_ls_shell.pdbx_fsc_free ? _refine_ls_shell.R_factor_R_free ? # _struct.entry_id 8J5A _struct.title 'Single-particle cryo-EM structure of mouse apoferritin at 1.19 Angstrom resolution (Dataset A)' _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 8J5A _struct_keywords.text 'single-particle cryo-EM, Cold field emission, CFEG, Apoferritin, CRYO ARM, STRUCTURAL PROTEIN' _struct_keywords.pdbx_keywords 'STRUCTURAL 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 ? C N N 3 ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 HIS A 9 ? ASP A 38 ? HIS A 13 ASP A 42 1 ? 30 HELX_P HELX_P2 AA2 LEU A 44 ? ARG A 72 ? LEU A 48 ARG A 76 1 ? 29 HELX_P HELX_P3 AA3 SER A 91 ? LYS A 120 ? SER A 95 LYS A 124 1 ? 30 HELX_P HELX_P4 AA4 ASP A 122 ? TYR A 133 ? ASP A 126 TYR A 137 1 ? 12 HELX_P HELX_P5 AA5 TYR A 133 ? GLY A 155 ? TYR A 137 GLY A 159 1 ? 23 HELX_P HELX_P6 AA6 ALA A 159 ? THR A 170 ? ALA A 163 THR A 174 1 ? 12 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # 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 GLU 58 OE1 ? ? ? 1_555 B NA . NA ? ? A GLU 62 A NA 201 1_555 ? ? ? ? ? ? ? 1.976 ? ? metalc2 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 321 1_555 ? ? ? ? ? ? ? 2.310 ? ? metalc3 metalc ? ? B NA . NA ? ? ? 1_555 C HOH . O ? ? A NA 201 A HOH 332 1_555 ? ? ? ? ? ? ? 2.188 ? ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ALA _struct_mon_prot_cis.label_seq_id 156 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id ALA _struct_mon_prot_cis.auth_seq_id 160 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 157 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 161 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -6.07 # _atom_sites.entry_id 8J5A _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 H N NA 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 PRO 1 5 5 PRO PRO A . n A 1 2 SER 2 6 6 SER SER A . n A 1 3 GLN 3 7 7 GLN GLN A . n A 1 4 VAL 4 8 8 VAL VAL A . n A 1 5 ARG 5 9 9 ARG ARG A . n A 1 6 GLN 6 10 10 GLN GLN A . n A 1 7 ASN 7 11 11 ASN ASN A . n A 1 8 TYR 8 12 12 TYR TYR A . n A 1 9 HIS 9 13 13 HIS HIS A . n A 1 10 GLN 10 14 14 GLN GLN A . n A 1 11 ASP 11 15 15 ASP ASP A . n A 1 12 ALA 12 16 16 ALA ALA A . n A 1 13 GLU 13 17 17 GLU GLU A . n A 1 14 ALA 14 18 18 ALA ALA A . n A 1 15 ALA 15 19 19 ALA ALA A . n A 1 16 ILE 16 20 20 ILE ILE A . n A 1 17 ASN 17 21 21 ASN ASN A . n A 1 18 ARG 18 22 22 ARG ARG A . n A 1 19 GLN 19 23 23 GLN GLN A . n A 1 20 ILE 20 24 24 ILE ILE A . n A 1 21 ASN 21 25 25 ASN ASN A . n A 1 22 LEU 22 26 26 LEU LEU A . n A 1 23 GLU 23 27 27 GLU GLU A . n A 1 24 LEU 24 28 28 LEU LEU A . n A 1 25 TYR 25 29 29 TYR TYR A . n A 1 26 ALA 26 30 30 ALA ALA A . n A 1 27 SER 27 31 31 SER SER A . n A 1 28 TYR 28 32 32 TYR TYR A . n A 1 29 VAL 29 33 33 VAL VAL A . n A 1 30 TYR 30 34 34 TYR TYR A . n A 1 31 LEU 31 35 35 LEU LEU A . n A 1 32 SER 32 36 36 SER SER A . n A 1 33 MET 33 37 37 MET MET A . n A 1 34 SER 34 38 38 SER SER A . n A 1 35 CYS 35 39 39 CYS CYS A . n A 1 36 TYR 36 40 40 TYR TYR A . n A 1 37 PHE 37 41 41 PHE PHE A . n A 1 38 ASP 38 42 42 ASP ASP A . n A 1 39 ARG 39 43 43 ARG ARG A . n A 1 40 ASP 40 44 44 ASP ASP A . n A 1 41 ASP 41 45 45 ASP ASP A . n A 1 42 VAL 42 46 46 VAL VAL A . n A 1 43 ALA 43 47 47 ALA ALA A . n A 1 44 LEU 44 48 48 LEU LEU A . n A 1 45 LYS 45 49 49 LYS LYS A . n A 1 46 ASN 46 50 50 ASN ASN A . n A 1 47 PHE 47 51 51 PHE PHE A . n A 1 48 ALA 48 52 52 ALA ALA A . n A 1 49 LYS 49 53 53 LYS LYS A . n A 1 50 TYR 50 54 54 TYR TYR A . n A 1 51 PHE 51 55 55 PHE PHE A . n A 1 52 LEU 52 56 56 LEU LEU A . n A 1 53 HIS 53 57 57 HIS HIS A . n A 1 54 GLN 54 58 58 GLN GLN A . n A 1 55 SER 55 59 59 SER SER A . n A 1 56 HIS 56 60 60 HIS HIS A . n A 1 57 GLU 57 61 61 GLU GLU A . n A 1 58 GLU 58 62 62 GLU GLU A . n A 1 59 ARG 59 63 63 ARG ARG A . n A 1 60 GLU 60 64 64 GLU GLU A . n A 1 61 HIS 61 65 65 HIS HIS A . n A 1 62 ALA 62 66 66 ALA ALA A . n A 1 63 GLU 63 67 67 GLU GLU A . n A 1 64 LYS 64 68 68 LYS LYS A . n A 1 65 LEU 65 69 69 LEU LEU A . n A 1 66 MET 66 70 70 MET MET A . n A 1 67 LYS 67 71 71 LYS LYS A . n A 1 68 LEU 68 72 72 LEU LEU A . n A 1 69 GLN 69 73 73 GLN GLN A . n A 1 70 ASN 70 74 74 ASN ASN A . n A 1 71 GLN 71 75 75 GLN GLN A . n A 1 72 ARG 72 76 76 ARG ARG A . n A 1 73 GLY 73 77 77 GLY GLY A . n A 1 74 GLY 74 78 78 GLY GLY A . n A 1 75 ARG 75 79 79 ARG ARG A . n A 1 76 ILE 76 80 80 ILE ILE A . n A 1 77 PHE 77 81 81 PHE PHE A . n A 1 78 LEU 78 82 82 LEU LEU A . n A 1 79 GLN 79 83 83 GLN GLN A . n A 1 80 ASP 80 84 84 ASP ASP A . n A 1 81 ILE 81 85 85 ILE ILE A . n A 1 82 LYS 82 86 86 LYS LYS A . n A 1 83 LYS 83 87 87 LYS LYS A . n A 1 84 PRO 84 88 88 PRO PRO A . n A 1 85 ASP 85 89 89 ASP ASP A . n A 1 86 ARG 86 90 90 ARG ARG A . n A 1 87 ASP 87 91 91 ASP ASP A . n A 1 88 ASP 88 92 92 ASP ASP A . n A 1 89 TRP 89 93 93 TRP TRP A . n A 1 90 GLU 90 94 94 GLU GLU A . n A 1 91 SER 91 95 95 SER SER A . n A 1 92 GLY 92 96 96 GLY GLY A . n A 1 93 LEU 93 97 97 LEU LEU A . n A 1 94 ASN 94 98 98 ASN ASN A . n A 1 95 ALA 95 99 99 ALA ALA A . n A 1 96 MET 96 100 100 MET MET A . n A 1 97 GLU 97 101 101 GLU GLU A . n A 1 98 CYS 98 102 102 CYS CYS A . n A 1 99 ALA 99 103 103 ALA ALA A . n A 1 100 LEU 100 104 104 LEU LEU A . n A 1 101 HIS 101 105 105 HIS HIS A . n A 1 102 LEU 102 106 106 LEU LEU A . n A 1 103 GLU 103 107 107 GLU GLU A . n A 1 104 LYS 104 108 108 LYS LYS A . n A 1 105 SER 105 109 109 SER SER A . n A 1 106 VAL 106 110 110 VAL VAL A . n A 1 107 ASN 107 111 111 ASN ASN A . n A 1 108 GLN 108 112 112 GLN GLN A . n A 1 109 SER 109 113 113 SER SER A . n A 1 110 LEU 110 114 114 LEU LEU A . n A 1 111 LEU 111 115 115 LEU LEU A . n A 1 112 GLU 112 116 116 GLU GLU A . n A 1 113 LEU 113 117 117 LEU LEU A . n A 1 114 HIS 114 118 118 HIS HIS A . n A 1 115 LYS 115 119 119 LYS LYS A . n A 1 116 LEU 116 120 120 LEU LEU A . n A 1 117 ALA 117 121 121 ALA ALA A . n A 1 118 THR 118 122 122 THR THR A . n A 1 119 ASP 119 123 123 ASP ASP A . n A 1 120 LYS 120 124 124 LYS LYS A . n A 1 121 ASN 121 125 125 ASN ASN A . n A 1 122 ASP 122 126 126 ASP ASP A . n A 1 123 PRO 123 127 127 PRO PRO A . n A 1 124 HIS 124 128 128 HIS HIS A . n A 1 125 LEU 125 129 129 LEU LEU A . n A 1 126 CYS 126 130 130 CYS CYS A . n A 1 127 ASP 127 131 131 ASP ASP A . n A 1 128 PHE 128 132 132 PHE PHE A . n A 1 129 ILE 129 133 133 ILE ILE A . n A 1 130 GLU 130 134 134 GLU GLU A . n A 1 131 THR 131 135 135 THR THR A . n A 1 132 TYR 132 136 136 TYR TYR A . n A 1 133 TYR 133 137 137 TYR TYR A . n A 1 134 LEU 134 138 138 LEU LEU A . n A 1 135 SER 135 139 139 SER SER A . n A 1 136 GLU 136 140 140 GLU GLU A . n A 1 137 GLN 137 141 141 GLN GLN A . n A 1 138 VAL 138 142 142 VAL VAL A . n A 1 139 LYS 139 143 143 LYS LYS A . n A 1 140 SER 140 144 144 SER SER A . n A 1 141 ILE 141 145 145 ILE ILE A . n A 1 142 LYS 142 146 146 LYS LYS A . n A 1 143 GLU 143 147 147 GLU GLU A . n A 1 144 LEU 144 148 148 LEU LEU A . n A 1 145 GLY 145 149 149 GLY GLY A . n A 1 146 ASP 146 150 150 ASP ASP A . n A 1 147 HIS 147 151 151 HIS HIS A . n A 1 148 VAL 148 152 152 VAL VAL A . n A 1 149 THR 149 153 153 THR THR A . n A 1 150 ASN 150 154 154 ASN ASN A . n A 1 151 LEU 151 155 155 LEU LEU A . n A 1 152 ARG 152 156 156 ARG ARG A . n A 1 153 LYS 153 157 157 LYS LYS A . n A 1 154 MET 154 158 158 MET MET A . n A 1 155 GLY 155 159 159 GLY GLY A . n A 1 156 ALA 156 160 160 ALA ALA A . n A 1 157 PRO 157 161 161 PRO PRO A . n A 1 158 GLU 158 162 162 GLU GLU A . n A 1 159 ALA 159 163 163 ALA ALA A . n A 1 160 GLY 160 164 164 GLY GLY A . n A 1 161 MET 161 165 165 MET MET A . n A 1 162 ALA 162 166 166 ALA ALA A . n A 1 163 GLU 163 167 167 GLU GLU A . n A 1 164 TYR 164 168 168 TYR TYR A . n A 1 165 LEU 165 169 169 LEU LEU A . n A 1 166 PHE 166 170 170 PHE PHE A . n A 1 167 ASP 167 171 171 ASP ASP A . n A 1 168 LYS 168 172 172 LYS LYS A . n A 1 169 HIS 169 173 173 HIS HIS A . n A 1 170 THR 170 174 174 THR THR A . n A 1 171 LEU 171 175 175 LEU LEU A . n A 1 172 GLY 172 176 176 GLY GLY A . n # _pdbx_contact_author.id 4 _pdbx_contact_author.email yone@spring8.or.jp _pdbx_contact_author.name_first Koji _pdbx_contact_author.name_last Yonekura _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-5520-4391 # 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 NA 1 201 201 NA NA A . C 3 HOH 1 301 331 HOH HOH A . C 3 HOH 2 302 413 HOH HOH A . C 3 HOH 3 303 407 HOH HOH A . C 3 HOH 4 304 340 HOH HOH A . C 3 HOH 5 305 402 HOH HOH A . C 3 HOH 6 306 323 HOH HOH A . C 3 HOH 7 307 447 HOH HOH A . C 3 HOH 8 308 318 HOH HOH A . C 3 HOH 9 309 314 HOH HOH A . C 3 HOH 10 310 301 HOH HOH A . C 3 HOH 11 311 305 HOH HOH A . C 3 HOH 12 312 437 HOH HOH A . C 3 HOH 13 313 433 HOH HOH A . C 3 HOH 14 314 309 HOH HOH A . C 3 HOH 15 315 312 HOH HOH A . C 3 HOH 16 316 394 HOH HOH A . C 3 HOH 17 317 310 HOH HOH A . C 3 HOH 18 318 303 HOH HOH A . C 3 HOH 19 319 422 HOH HOH A . C 3 HOH 20 320 436 HOH HOH A . C 3 HOH 21 321 311 HOH HOH A . C 3 HOH 22 322 316 HOH HOH A . C 3 HOH 23 323 398 HOH HOH A . C 3 HOH 24 324 320 HOH HOH A . C 3 HOH 25 325 405 HOH HOH A . C 3 HOH 26 326 423 HOH HOH A . C 3 HOH 27 327 304 HOH HOH A . C 3 HOH 28 328 325 HOH HOH A . C 3 HOH 29 329 306 HOH HOH A . C 3 HOH 30 330 330 HOH HOH A . C 3 HOH 31 331 313 HOH HOH A . C 3 HOH 32 332 307 HOH HOH A . C 3 HOH 33 333 324 HOH HOH A . C 3 HOH 34 334 344 HOH HOH A . C 3 HOH 35 335 409 HOH HOH A . C 3 HOH 36 336 315 HOH HOH A . C 3 HOH 37 337 425 HOH HOH A . C 3 HOH 38 338 408 HOH HOH A . C 3 HOH 39 339 333 HOH HOH A . C 3 HOH 40 340 349 HOH HOH A . C 3 HOH 41 341 334 HOH HOH A . C 3 HOH 42 342 338 HOH HOH A . C 3 HOH 43 343 424 HOH HOH A . C 3 HOH 44 344 326 HOH HOH A . C 3 HOH 45 345 434 HOH HOH A . C 3 HOH 46 346 329 HOH HOH A . C 3 HOH 47 347 343 HOH HOH A . C 3 HOH 48 348 319 HOH HOH A . C 3 HOH 49 349 332 HOH HOH A . C 3 HOH 50 350 337 HOH HOH A . C 3 HOH 51 351 328 HOH HOH A . C 3 HOH 52 352 335 HOH HOH A . C 3 HOH 53 353 350 HOH HOH A . C 3 HOH 54 354 317 HOH HOH A . C 3 HOH 55 355 426 HOH HOH A . C 3 HOH 56 356 435 HOH HOH A . C 3 HOH 57 357 351 HOH HOH A . C 3 HOH 58 358 302 HOH HOH A . C 3 HOH 59 359 339 HOH HOH A . C 3 HOH 60 360 412 HOH HOH A . C 3 HOH 61 361 428 HOH HOH A . C 3 HOH 62 362 399 HOH HOH A . C 3 HOH 63 363 341 HOH HOH A . C 3 HOH 64 364 360 HOH HOH A . C 3 HOH 65 365 355 HOH HOH A . C 3 HOH 66 366 342 HOH HOH A . C 3 HOH 67 367 336 HOH HOH A . C 3 HOH 68 368 345 HOH HOH A . C 3 HOH 69 369 348 HOH HOH A . C 3 HOH 70 370 352 HOH HOH A . C 3 HOH 71 371 365 HOH HOH A . C 3 HOH 72 372 448 HOH HOH A . C 3 HOH 73 373 444 HOH HOH A . C 3 HOH 74 374 354 HOH HOH A . C 3 HOH 75 375 353 HOH HOH A . C 3 HOH 76 376 347 HOH HOH A . C 3 HOH 77 377 363 HOH HOH A . C 3 HOH 78 378 356 HOH HOH A . C 3 HOH 79 379 366 HOH HOH A . C 3 HOH 80 380 404 HOH HOH A . C 3 HOH 81 381 308 HOH HOH A . C 3 HOH 82 382 362 HOH HOH A . C 3 HOH 83 383 401 HOH HOH A . C 3 HOH 84 384 427 HOH HOH A . C 3 HOH 85 385 359 HOH HOH A . C 3 HOH 86 386 358 HOH HOH A . C 3 HOH 87 387 376 HOH HOH A . C 3 HOH 88 388 322 HOH HOH A . C 3 HOH 89 389 361 HOH HOH A . C 3 HOH 90 390 400 HOH HOH A . C 3 HOH 91 391 327 HOH HOH A . C 3 HOH 92 392 369 HOH HOH A . C 3 HOH 93 393 406 HOH HOH A . C 3 HOH 94 394 368 HOH HOH A . C 3 HOH 95 395 357 HOH HOH A . C 3 HOH 96 396 370 HOH HOH A . C 3 HOH 97 397 414 HOH HOH A . C 3 HOH 98 398 415 HOH HOH A . C 3 HOH 99 399 367 HOH HOH A . C 3 HOH 100 400 445 HOH HOH A . C 3 HOH 101 401 440 HOH HOH A . C 3 HOH 102 402 373 HOH HOH A . C 3 HOH 103 403 364 HOH HOH A . C 3 HOH 104 404 321 HOH HOH A . C 3 HOH 105 405 396 HOH HOH A . C 3 HOH 106 406 374 HOH HOH A . C 3 HOH 107 407 379 HOH HOH A . C 3 HOH 108 408 375 HOH HOH A . C 3 HOH 109 409 377 HOH HOH A . C 3 HOH 110 410 378 HOH HOH A . C 3 HOH 111 411 395 HOH HOH A . C 3 HOH 112 412 371 HOH HOH A . C 3 HOH 113 413 429 HOH HOH A . C 3 HOH 114 414 346 HOH HOH A . C 3 HOH 115 415 384 HOH HOH A . C 3 HOH 116 416 386 HOH HOH A . C 3 HOH 117 417 380 HOH HOH A . C 3 HOH 118 418 381 HOH HOH A . C 3 HOH 119 419 417 HOH HOH A . C 3 HOH 120 420 439 HOH HOH A . C 3 HOH 121 421 393 HOH HOH A . C 3 HOH 122 422 431 HOH HOH A . C 3 HOH 123 423 446 HOH HOH A . C 3 HOH 124 424 430 HOH HOH A . C 3 HOH 125 425 382 HOH HOH A . C 3 HOH 126 426 443 HOH HOH A . C 3 HOH 127 427 410 HOH HOH A . C 3 HOH 128 428 383 HOH HOH A . C 3 HOH 129 429 385 HOH HOH A . C 3 HOH 130 430 420 HOH HOH A . C 3 HOH 131 431 392 HOH HOH A . C 3 HOH 132 432 403 HOH HOH A . C 3 HOH 133 433 419 HOH HOH A . C 3 HOH 134 434 397 HOH HOH A . C 3 HOH 135 435 372 HOH HOH A . C 3 HOH 136 436 389 HOH HOH A . C 3 HOH 137 437 441 HOH HOH A . C 3 HOH 138 438 390 HOH HOH A . C 3 HOH 139 439 388 HOH HOH A . C 3 HOH 140 440 418 HOH HOH A . C 3 HOH 141 441 391 HOH HOH A . # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'complete point assembly' ? 24-meric 24 2 'point asymmetric unit' ? monomeric 1 3 'point asymmetric unit, std point frame' ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-24)' A,B,C 2 1 A,B,C 3 P A,B,C # 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] P 'transform to point frame' ? ? -1.00000000 0.00000000 0.00000000 63.36000 0.00000000 0.00000000 -1.00000000 63.36000 0.00000000 -1.00000000 0.00000000 63.36000 1 'identity operation' 1_555 x,y,z 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 2 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 126.72000 3 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 -1.00000000 0.00000000 126.72000 0.00000000 0.00000000 1.00000000 0.00000 4 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 126.72000 0.00000000 0.00000000 -1.00000000 126.72000 5 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 6 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 126.72000 -1.00000000 0.00000000 0.00000000 126.72000 7 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 126.72000 0.00000000 0.00000000 1.00000000 0.00000 -1.00000000 0.00000000 0.00000000 126.72000 8 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 126.72000 0.00000000 0.00000000 -1.00000000 126.72000 1.00000000 0.00000000 0.00000000 0.00000 9 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 10 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 126.72000 -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 1.00000000 0.00000000 0.00000 11 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 -1.00000000 0.00000000 126.72000 12 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 126.72000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 -1.00000000 0.00000000 126.72000 13 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 -1.00000000 0.00000000 126.72000 1.00000000 0.00000000 0.00000000 0.00000 14 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 126.72000 0.00000000 -1.00000000 0.00000000 126.72000 -1.00000000 0.00000000 0.00000000 126.72000 15 'point symmetry operation' ? ? 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 126.72000 16 'point symmetry operation' ? ? 0.00000000 0.00000000 -1.00000000 126.72000 0.00000000 1.00000000 0.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 17 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 126.72000 0.00000000 1.00000000 0.00000000 0.00000 18 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 1.00000000 0.00000000 0.00000 19 'point symmetry operation' ? ? -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 0.00000000 -1.00000000 126.72000 0.00000000 -1.00000000 0.00000000 126.72000 20 'point symmetry operation' ? ? 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 0.00000000 -1.00000000 0.00000000 126.72000 21 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 0.00000000 1.00000000 0.00000 22 'point symmetry operation' ? ? 0.00000000 1.00000000 0.00000000 0.00000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 -1.00000000 126.72000 23 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 126.72000 1.00000000 0.00000000 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 24 'point symmetry operation' ? ? 0.00000000 -1.00000000 0.00000000 126.72000 -1.00000000 0.00000000 0.00000000 126.72000 0.00000000 0.00000000 -1.00000000 126.72000 # _pdbx_point_symmetry.entry_id 8J5A _pdbx_point_symmetry.Schoenflies_symbol O # 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 OE1 ? A GLU 58 ? A GLU 62 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 321 ? 1_555 149.5 ? 2 OE1 ? A GLU 58 ? A GLU 62 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 332 ? 1_555 79.2 ? 3 O ? C HOH . ? A HOH 321 ? 1_555 NA ? B NA . ? A NA 201 ? 1_555 O ? C HOH . ? A HOH 332 ? 1_555 76.0 ? # _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 2023-07-12 # _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 ? # _software.citation_id ? _software.classification refinement _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 REFMAC _software.os ? _software.os_version ? _software.type ? _software.version 5.8.0267 _software.pdbx_ordinal 1 # _pdbx_entry_details.entry_id 8J5A _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 Y # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 8J5A _em_3d_fitting.method ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_space ? _em_3d_fitting.ref_protocol ? # _em_3d_reconstruction.entry_id 8J5A _em_3d_reconstruction.id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.citation_id ? _em_3d_reconstruction.details ? _em_3d_reconstruction.resolution 1.19 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.nominal_pixel_size ? _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.num_particles 2235864 _em_3d_reconstruction.euler_angles_details ? _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.refinement_type ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.symmetry_type POINT # _em_buffer.id 1 _em_buffer.specimen_id 1 _em_buffer.name ? _em_buffer.details ? _em_buffer.pH 7.5 # _em_entity_assembly.id 1 _em_entity_assembly.parent_id 0 _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.name 'Apoferritin from Mus musculus' _em_entity_assembly.details ? _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? _em_entity_assembly.entity_id_list 1 # _em_imaging.entry_id 8J5A _em_imaging.id 1 _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.residual_tilt ? _em_imaging.microscope_model 'JEOL CRYO ARM 300' _em_imaging.specimen_holder_type ? _em_imaging.specimen_holder_model ? _em_imaging.details ? _em_imaging.date ? _em_imaging.accelerating_voltage 300 _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_min 500 _em_imaging.nominal_defocus_max 1000 _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_defocus_max ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.nominal_magnification ? _em_imaging.calibrated_magnification ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.citation_id ? _em_imaging.temperature ? _em_imaging.detector_distance ? _em_imaging.recording_temperature_minimum ? _em_imaging.recording_temperature_maximum ? _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter 150 _em_imaging.specimen_id 1 _em_imaging.cryogen ? # _em_vitrification.entry_id 8J5A _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.cryogen_name NITROGEN _em_vitrification.humidity ? _em_vitrification.temp ? _em_vitrification.chamber_temperature ? _em_vitrification.instrument ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? _em_vitrification.details ? # _em_experiment.entry_id 8J5A _em_experiment.id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 ND1 _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 HIS _pdbx_validate_close_contact.auth_seq_id_1 173 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 A _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 301 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.14 # 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 VAL A 46 ? ? -123.02 -60.64 2 1 GLU A 94 ? ? 79.97 -52.72 # 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 A GLN 14 ? CG ? A GLN 10 CG 2 1 Y 1 A GLN 14 ? CD ? A GLN 10 CD 3 1 Y 1 A GLN 14 ? OE1 ? A GLN 10 OE1 4 1 Y 1 A GLN 14 ? NE2 ? A GLN 10 NE2 5 1 Y 1 A ASP 42 ? CG ? A ASP 38 CG 6 1 Y 1 A ASP 42 ? OD1 ? A ASP 38 OD1 7 1 Y 1 A ASP 42 ? OD2 ? A ASP 38 OD2 8 1 Y 1 A LYS 49 ? CG ? A LYS 45 CG 9 1 Y 1 A LYS 49 ? CD ? A LYS 45 CD 10 1 Y 1 A LYS 49 ? CE ? A LYS 45 CE 11 1 Y 1 A LYS 49 ? NZ ? A LYS 45 NZ 12 1 Y 1 A LYS 53 ? CG ? A LYS 49 CG 13 1 Y 1 A LYS 53 ? CD ? A LYS 49 CD 14 1 Y 1 A LYS 53 ? CE ? A LYS 49 CE 15 1 Y 1 A LYS 53 ? NZ ? A LYS 49 NZ 16 1 Y 1 A GLU 61 ? CG ? A GLU 57 CG 17 1 Y 1 A GLU 61 ? CD ? A GLU 57 CD 18 1 Y 1 A GLU 61 ? OE1 ? A GLU 57 OE1 19 1 Y 1 A GLU 61 ? OE2 ? A GLU 57 OE2 20 1 Y 1 A GLU 64 ? CG ? A GLU 60 CG 21 1 Y 1 A GLU 64 ? CD ? A GLU 60 CD 22 1 Y 1 A GLU 64 ? OE1 ? A GLU 60 OE1 23 1 Y 1 A GLU 64 ? OE2 ? A GLU 60 OE2 24 1 Y 1 A LYS 71 ? CG ? A LYS 67 CG 25 1 Y 1 A LYS 71 ? CD ? A LYS 67 CD 26 1 Y 1 A LYS 71 ? CE ? A LYS 67 CE 27 1 Y 1 A LYS 71 ? NZ ? A LYS 67 NZ 28 1 Y 1 A LYS 86 ? CG ? A LYS 82 CG 29 1 Y 1 A LYS 86 ? CD ? A LYS 82 CD 30 1 Y 1 A LYS 86 ? CE ? A LYS 82 CE 31 1 Y 1 A LYS 86 ? NZ ? A LYS 82 NZ 32 1 Y 1 A ASP 89 ? CG ? A ASP 85 CG 33 1 Y 1 A ASP 89 ? OD1 ? A ASP 85 OD1 34 1 Y 1 A ASP 89 ? OD2 ? A ASP 85 OD2 35 1 Y 1 A ARG 90 ? CG ? A ARG 86 CG 36 1 Y 1 A ARG 90 ? CD ? A ARG 86 CD 37 1 Y 1 A ARG 90 ? NE ? A ARG 86 NE 38 1 Y 1 A ARG 90 ? CZ ? A ARG 86 CZ 39 1 Y 1 A ARG 90 ? NH1 ? A ARG 86 NH1 40 1 Y 1 A ARG 90 ? NH2 ? A ARG 86 NH2 41 1 Y 1 A ASP 91 ? CG ? A ASP 87 CG 42 1 Y 1 A ASP 91 ? OD1 ? A ASP 87 OD1 43 1 Y 1 A ASP 91 ? OD2 ? A ASP 87 OD2 44 1 Y 1 A GLU 94 ? CG ? A GLU 90 CG 45 1 Y 1 A GLU 94 ? CD ? A GLU 90 CD 46 1 Y 1 A GLU 94 ? OE1 ? A GLU 90 OE1 47 1 Y 1 A GLU 94 ? OE2 ? A GLU 90 OE2 48 1 Y 1 A GLU 116 ? CG ? A GLU 112 CG 49 1 Y 1 A GLU 116 ? CD ? A GLU 112 CD 50 1 Y 1 A GLU 116 ? OE1 ? A GLU 112 OE1 51 1 Y 1 A GLU 116 ? OE2 ? A GLU 112 OE2 52 1 Y 1 A LYS 119 ? CG ? A LYS 115 CG 53 1 Y 1 A LYS 119 ? CD ? A LYS 115 CD 54 1 Y 1 A LYS 119 ? CE ? A LYS 115 CE 55 1 Y 1 A LYS 119 ? NZ ? A LYS 115 NZ 56 1 Y 1 A GLU 140 ? CG ? A GLU 136 CG 57 1 Y 1 A GLU 140 ? CD ? A GLU 136 CD 58 1 Y 1 A GLU 140 ? OE1 ? A GLU 136 OE1 59 1 Y 1 A GLU 140 ? OE2 ? A GLU 136 OE2 60 1 Y 1 A LYS 143 ? CG ? A LYS 139 CG 61 1 Y 1 A LYS 143 ? CD ? A LYS 139 CD 62 1 Y 1 A LYS 143 ? CE ? A LYS 139 CE 63 1 Y 1 A LYS 143 ? NZ ? A LYS 139 NZ 64 1 Y 1 A GLU 147 ? CG ? A GLU 143 CG 65 1 Y 1 A GLU 147 ? CD ? A GLU 143 CD 66 1 Y 1 A GLU 147 ? OE1 ? A GLU 143 OE1 67 1 Y 1 A GLU 147 ? OE2 ? A GLU 143 OE2 68 1 Y 1 A LYS 157 ? CG ? A LYS 153 CG 69 1 Y 1 A LYS 157 ? CD ? A LYS 153 CD 70 1 Y 1 A LYS 157 ? CE ? A LYS 153 CE 71 1 Y 1 A LYS 157 ? NZ ? A LYS 153 NZ 72 1 Y 1 A GLU 162 ? CG ? A GLU 158 CG 73 1 Y 1 A GLU 162 ? CD ? A GLU 158 CD 74 1 Y 1 A GLU 162 ? OE1 ? A GLU 158 OE1 75 1 Y 1 A GLU 162 ? OE2 ? A GLU 158 OE2 # _em_ctf_correction.details ? _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' # _em_entity_assembly_naturalsource.cell ? _em_entity_assembly_naturalsource.cellular_location ? _em_entity_assembly_naturalsource.entity_assembly_id 1 _em_entity_assembly_naturalsource.id 2 _em_entity_assembly_naturalsource.ncbi_tax_id 10090 _em_entity_assembly_naturalsource.organism 'Mus musculus' _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.ncbi_tax_id 562 _em_entity_assembly_recombinant.organism 'Escherichia coli' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _em_image_processing.details ? _em_image_processing.id 1 _em_image_processing.image_recording_id 1 # _em_image_recording.average_exposure_time ? _em_image_recording.avg_electron_dose_per_subtomogram ? _em_image_recording.avg_electron_dose_per_image 36.47 _em_image_recording.details ? _em_image_recording.detector_mode ? _em_image_recording.film_or_detector_model 'GATAN K3 (6k x 4k)' _em_image_recording.id 1 _em_image_recording.imaging_id 1 _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # loop_ _em_software.category _em_software.details _em_software.id _em_software.image_processing_id _em_software.fitting_id _em_software.imaging_id _em_software.name _em_software.version 'PARTICLE SELECTION' ? 1 1 ? ? ? ? 'IMAGE ACQUISITION' ? 2 ? ? 1 ? ? MASKING ? 3 ? ? ? ? ? 'CTF CORRECTION' ? 4 1 ? ? ? ? 'LAYERLINE INDEXING' ? 5 ? ? ? ? ? 'DIFFRACTION INDEXING' ? 6 ? ? ? ? ? 'MODEL FITTING' ? 7 ? 1 ? 'UCSF Chimera' 1.15 'MODEL FITTING' ? 8 ? 1 ? Coot 0.9.6 OTHER ? 9 ? ? ? ? ? 'MODEL REFINEMENT' ? 10 ? 1 ? REFMAC 5.8.0267 'INITIAL EULER ASSIGNMENT' ? 11 1 ? ? ? ? 'FINAL EULER ASSIGNMENT' ? 12 1 ? ? ? ? CLASSIFICATION ? 13 1 ? ? ? ? RECONSTRUCTION ? 14 1 ? ? RELION 3.1 'VOLUME SELECTION' ? 15 1 1 1 ? ? 'SERIES ALIGNMENT' ? 16 1 1 1 ? ? 'MOLECULAR REPLACEMENT' ? 17 1 1 1 ? ? 'LATTICE DISTORTION CORRECTION' ? 18 1 1 1 ? ? 'SYMMETRY DETERMINATION' ? 19 1 1 1 ? ? 'CRYSTALLOGRAPHY MERGING' ? 20 1 1 1 ? ? # _em_specimen.concentration ? _em_specimen.details ? _em_specimen.embedding_applied NO _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.shadowing_applied NO _em_specimen.staining_applied NO _em_specimen.vitrification_applied YES # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Japan Society for the Promotion of Science (JSPS)' Japan JPMJMI20G5 1 'Japan Society for the Promotion of Science (JSPS)' Japan JPMJCR18J2 2 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id NA _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id NA _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'SODIUM ION' NA 3 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support microscopy _pdbx_struct_assembly_auth_evidence.details ? #