data_8DNA # _entry.id 8DNA # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.393 _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 8DNA pdb_00008dna 10.2210/pdb8dna/pdb WWPDB D_1000266868 ? ? EMDB EMD-27560 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2023-03-22 2 'Structure model' 1 1 2024-06-12 # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Data collection' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 8DNA _pdbx_database_status.recvd_initial_deposition_date 2022-07-11 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'Acidopropionibacterium acidopropionici encapsulin in a closed state at pH 3.0' _pdbx_database_related.db_id EMD-27560 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_contact_author.id 3 _pdbx_contact_author.email tgiessen@umich.edu _pdbx_contact_author.name_first Tobias _pdbx_contact_author.name_last Giessen _pdbx_contact_author.name_mi W. _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-6328-2031 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Jones, J.A.' 1 0000-0001-8006-5661 'Andreas, M.P.' 2 0000-0001-8871-3053 'Giessen, T.W.' 3 0000-0001-6328-2031 # _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 Biomacromolecules _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 1526-4602 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 24 _citation.language ? _citation.page_first 1388 _citation.page_last 1399 _citation.title 'Exploring the Extreme Acid Tolerance of a Dynamic Protein Nanocage.' _citation.year 2023 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1021/acs.biomac.2c01424 _citation.pdbx_database_id_PubMed 36796007 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jones, J.A.' 1 0000-0001-8006-5661 primary 'Andreas, M.P.' 2 0000-0001-8871-3053 primary 'Giessen, T.W.' 3 0000-0001-6328-2031 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description '29 kDa antigen cfp29' _entity.formula_weight 28522.725 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name Encapsulin # _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 ;MNNLHRELAPISEAAWKQIDDEARDTFSLRAAGRRVVDVPEPAGPTLGSVSLGHLETGSQTDGVQTSVYRVQPLVQVRVP FTVSRADIDDVERGAVDLTWDPVDDAVAKLVDTEDTAILHGWEEAGITGLSEASVHQPVQMPAELEQIDDAVSGACNVLR LADVEGPYDLVLPQQLYTQVSETTDHGVPVVDHLTQLLSGGEVLWAPAARCALVVSRRGGDSCLFLGRDVSIGYLSHDAQ TVTLYLEESFTFRVHQPDAAVALV ; _entity_poly.pdbx_seq_one_letter_code_can ;MNNLHRELAPISEAAWKQIDDEARDTFSLRAAGRRVVDVPEPAGPTLGSVSLGHLETGSQTDGVQTSVYRVQPLVQVRVP FTVSRADIDDVERGAVDLTWDPVDDAVAKLVDTEDTAILHGWEEAGITGLSEASVHQPVQMPAELEQIDDAVSGACNVLR LADVEGPYDLVLPQQLYTQVSETTDHGVPVVDHLTQLLSGGEVLWAPAARCALVVSRRGGDSCLFLGRDVSIGYLSHDAQ TVTLYLEESFTFRVHQPDAAVALV ; _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 MET n 1 2 ASN n 1 3 ASN n 1 4 LEU n 1 5 HIS n 1 6 ARG n 1 7 GLU n 1 8 LEU n 1 9 ALA n 1 10 PRO n 1 11 ILE n 1 12 SER n 1 13 GLU n 1 14 ALA n 1 15 ALA n 1 16 TRP n 1 17 LYS n 1 18 GLN n 1 19 ILE n 1 20 ASP n 1 21 ASP n 1 22 GLU n 1 23 ALA n 1 24 ARG n 1 25 ASP n 1 26 THR n 1 27 PHE n 1 28 SER n 1 29 LEU n 1 30 ARG n 1 31 ALA n 1 32 ALA n 1 33 GLY n 1 34 ARG n 1 35 ARG n 1 36 VAL n 1 37 VAL n 1 38 ASP n 1 39 VAL n 1 40 PRO n 1 41 GLU n 1 42 PRO n 1 43 ALA n 1 44 GLY n 1 45 PRO n 1 46 THR n 1 47 LEU n 1 48 GLY n 1 49 SER n 1 50 VAL n 1 51 SER n 1 52 LEU n 1 53 GLY n 1 54 HIS n 1 55 LEU n 1 56 GLU n 1 57 THR n 1 58 GLY n 1 59 SER n 1 60 GLN n 1 61 THR n 1 62 ASP n 1 63 GLY n 1 64 VAL n 1 65 GLN n 1 66 THR n 1 67 SER n 1 68 VAL n 1 69 TYR n 1 70 ARG n 1 71 VAL n 1 72 GLN n 1 73 PRO n 1 74 LEU n 1 75 VAL n 1 76 GLN n 1 77 VAL n 1 78 ARG n 1 79 VAL n 1 80 PRO n 1 81 PHE n 1 82 THR n 1 83 VAL n 1 84 SER n 1 85 ARG n 1 86 ALA n 1 87 ASP n 1 88 ILE n 1 89 ASP n 1 90 ASP n 1 91 VAL n 1 92 GLU n 1 93 ARG n 1 94 GLY n 1 95 ALA n 1 96 VAL n 1 97 ASP n 1 98 LEU n 1 99 THR n 1 100 TRP n 1 101 ASP n 1 102 PRO n 1 103 VAL n 1 104 ASP n 1 105 ASP n 1 106 ALA n 1 107 VAL n 1 108 ALA n 1 109 LYS n 1 110 LEU n 1 111 VAL n 1 112 ASP n 1 113 THR n 1 114 GLU n 1 115 ASP n 1 116 THR n 1 117 ALA n 1 118 ILE n 1 119 LEU n 1 120 HIS n 1 121 GLY n 1 122 TRP n 1 123 GLU n 1 124 GLU n 1 125 ALA n 1 126 GLY n 1 127 ILE n 1 128 THR n 1 129 GLY n 1 130 LEU n 1 131 SER n 1 132 GLU n 1 133 ALA n 1 134 SER n 1 135 VAL n 1 136 HIS n 1 137 GLN n 1 138 PRO n 1 139 VAL n 1 140 GLN n 1 141 MET n 1 142 PRO n 1 143 ALA n 1 144 GLU n 1 145 LEU n 1 146 GLU n 1 147 GLN n 1 148 ILE n 1 149 ASP n 1 150 ASP n 1 151 ALA n 1 152 VAL n 1 153 SER n 1 154 GLY n 1 155 ALA n 1 156 CYS n 1 157 ASN n 1 158 VAL n 1 159 LEU n 1 160 ARG n 1 161 LEU n 1 162 ALA n 1 163 ASP n 1 164 VAL n 1 165 GLU n 1 166 GLY n 1 167 PRO n 1 168 TYR n 1 169 ASP n 1 170 LEU n 1 171 VAL n 1 172 LEU n 1 173 PRO n 1 174 GLN n 1 175 GLN n 1 176 LEU n 1 177 TYR n 1 178 THR n 1 179 GLN n 1 180 VAL n 1 181 SER n 1 182 GLU n 1 183 THR n 1 184 THR n 1 185 ASP n 1 186 HIS n 1 187 GLY n 1 188 VAL n 1 189 PRO n 1 190 VAL n 1 191 VAL n 1 192 ASP n 1 193 HIS n 1 194 LEU n 1 195 THR n 1 196 GLN n 1 197 LEU n 1 198 LEU n 1 199 SER n 1 200 GLY n 1 201 GLY n 1 202 GLU n 1 203 VAL n 1 204 LEU n 1 205 TRP n 1 206 ALA n 1 207 PRO n 1 208 ALA n 1 209 ALA n 1 210 ARG n 1 211 CYS n 1 212 ALA n 1 213 LEU n 1 214 VAL n 1 215 VAL n 1 216 SER n 1 217 ARG n 1 218 ARG n 1 219 GLY n 1 220 GLY n 1 221 ASP n 1 222 SER n 1 223 CYS n 1 224 LEU n 1 225 PHE n 1 226 LEU n 1 227 GLY n 1 228 ARG n 1 229 ASP n 1 230 VAL n 1 231 SER n 1 232 ILE n 1 233 GLY n 1 234 TYR n 1 235 LEU n 1 236 SER n 1 237 HIS n 1 238 ASP n 1 239 ALA n 1 240 GLN n 1 241 THR n 1 242 VAL n 1 243 THR n 1 244 LEU n 1 245 TYR n 1 246 LEU n 1 247 GLU n 1 248 GLU n 1 249 SER n 1 250 PHE n 1 251 THR n 1 252 PHE n 1 253 ARG n 1 254 VAL n 1 255 HIS n 1 256 GLN n 1 257 PRO n 1 258 ASP n 1 259 ALA n 1 260 ALA n 1 261 VAL n 1 262 ALA n 1 263 LEU n 1 264 VAL 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 264 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene PACID_10050 _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'ATCC 4875 / DSM 20272 / JCM 6432 / NBRC 12425 / NCIMB 8070 / 4' _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 'Acidipropionibacterium acidipropionici ATCC 4875' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1171373 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'BL21(DE3)' _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 ? # 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 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 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 # 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 MET 1 1 1 MET MET A . n A 1 2 ASN 2 2 2 ASN ASN A . n A 1 3 ASN 3 3 3 ASN ASN A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 HIS 5 5 5 HIS HIS A . n A 1 6 ARG 6 6 6 ARG ARG A . n A 1 7 GLU 7 7 7 GLU GLU A . n A 1 8 LEU 8 8 8 LEU LEU A . n A 1 9 ALA 9 9 9 ALA ALA A . n A 1 10 PRO 10 10 10 PRO PRO A . n A 1 11 ILE 11 11 11 ILE ILE A . n A 1 12 SER 12 12 12 SER SER A . n A 1 13 GLU 13 13 13 GLU GLU A . n A 1 14 ALA 14 14 14 ALA ALA A . n A 1 15 ALA 15 15 15 ALA ALA A . n A 1 16 TRP 16 16 16 TRP TRP A . n A 1 17 LYS 17 17 17 LYS LYS A . n A 1 18 GLN 18 18 18 GLN GLN A . n A 1 19 ILE 19 19 19 ILE ILE A . n A 1 20 ASP 20 20 20 ASP ASP A . n A 1 21 ASP 21 21 21 ASP ASP A . n A 1 22 GLU 22 22 22 GLU GLU A . n A 1 23 ALA 23 23 23 ALA ALA A . n A 1 24 ARG 24 24 24 ARG ARG A . n A 1 25 ASP 25 25 25 ASP ASP A . n A 1 26 THR 26 26 26 THR THR A . n A 1 27 PHE 27 27 27 PHE PHE A . n A 1 28 SER 28 28 28 SER SER A . n A 1 29 LEU 29 29 29 LEU LEU A . n A 1 30 ARG 30 30 30 ARG ARG A . n A 1 31 ALA 31 31 31 ALA ALA A . n A 1 32 ALA 32 32 32 ALA ALA A . n A 1 33 GLY 33 33 33 GLY GLY A . n A 1 34 ARG 34 34 34 ARG ARG A . n A 1 35 ARG 35 35 35 ARG ARG A . n A 1 36 VAL 36 36 36 VAL VAL A . n A 1 37 VAL 37 37 37 VAL VAL A . n A 1 38 ASP 38 38 38 ASP ASP A . n A 1 39 VAL 39 39 39 VAL VAL A . n A 1 40 PRO 40 40 40 PRO PRO A . n A 1 41 GLU 41 41 41 GLU GLU A . n A 1 42 PRO 42 42 42 PRO PRO A . n A 1 43 ALA 43 43 43 ALA ALA A . n A 1 44 GLY 44 44 44 GLY GLY A . n A 1 45 PRO 45 45 45 PRO PRO A . n A 1 46 THR 46 46 46 THR THR A . n A 1 47 LEU 47 47 47 LEU LEU A . n A 1 48 GLY 48 48 48 GLY GLY A . n A 1 49 SER 49 49 49 SER SER A . n A 1 50 VAL 50 50 50 VAL VAL A . n A 1 51 SER 51 51 51 SER SER A . n A 1 52 LEU 52 52 52 LEU LEU A . n A 1 53 GLY 53 53 53 GLY GLY A . n A 1 54 HIS 54 54 54 HIS HIS A . n A 1 55 LEU 55 55 55 LEU LEU A . n A 1 56 GLU 56 56 56 GLU GLU A . n A 1 57 THR 57 57 57 THR THR A . n A 1 58 GLY 58 58 58 GLY GLY A . n A 1 59 SER 59 59 59 SER SER A . n A 1 60 GLN 60 60 60 GLN GLN A . n A 1 61 THR 61 61 61 THR THR A . n A 1 62 ASP 62 62 62 ASP ASP A . n A 1 63 GLY 63 63 63 GLY GLY A . n A 1 64 VAL 64 64 64 VAL VAL A . n A 1 65 GLN 65 65 65 GLN GLN A . n A 1 66 THR 66 66 66 THR THR A . n A 1 67 SER 67 67 67 SER SER A . n A 1 68 VAL 68 68 68 VAL VAL A . n A 1 69 TYR 69 69 69 TYR TYR A . n A 1 70 ARG 70 70 70 ARG ARG A . n A 1 71 VAL 71 71 71 VAL VAL A . n A 1 72 GLN 72 72 72 GLN GLN A . n A 1 73 PRO 73 73 73 PRO PRO A . n A 1 74 LEU 74 74 74 LEU LEU A . n A 1 75 VAL 75 75 75 VAL VAL A . n A 1 76 GLN 76 76 76 GLN GLN A . n A 1 77 VAL 77 77 77 VAL VAL A . n A 1 78 ARG 78 78 78 ARG ARG A . n A 1 79 VAL 79 79 79 VAL VAL A . n A 1 80 PRO 80 80 80 PRO PRO A . n A 1 81 PHE 81 81 81 PHE PHE A . n A 1 82 THR 82 82 82 THR THR A . n A 1 83 VAL 83 83 83 VAL VAL A . n A 1 84 SER 84 84 84 SER SER A . n A 1 85 ARG 85 85 85 ARG ARG A . n A 1 86 ALA 86 86 86 ALA ALA A . n A 1 87 ASP 87 87 87 ASP ASP A . n A 1 88 ILE 88 88 88 ILE ILE A . n A 1 89 ASP 89 89 89 ASP ASP A . n A 1 90 ASP 90 90 90 ASP ASP A . n A 1 91 VAL 91 91 91 VAL VAL A . n A 1 92 GLU 92 92 92 GLU GLU A . n A 1 93 ARG 93 93 93 ARG ARG A . n A 1 94 GLY 94 94 94 GLY GLY A . n A 1 95 ALA 95 95 95 ALA ALA A . n A 1 96 VAL 96 96 96 VAL VAL A . n A 1 97 ASP 97 97 97 ASP ASP A . n A 1 98 LEU 98 98 98 LEU LEU A . n A 1 99 THR 99 99 99 THR THR A . n A 1 100 TRP 100 100 100 TRP TRP A . n A 1 101 ASP 101 101 101 ASP ASP A . n A 1 102 PRO 102 102 102 PRO PRO A . n A 1 103 VAL 103 103 103 VAL VAL A . n A 1 104 ASP 104 104 104 ASP ASP A . n A 1 105 ASP 105 105 105 ASP ASP A . n A 1 106 ALA 106 106 106 ALA ALA A . n A 1 107 VAL 107 107 107 VAL VAL A . n A 1 108 ALA 108 108 108 ALA ALA A . n A 1 109 LYS 109 109 109 LYS LYS A . n A 1 110 LEU 110 110 110 LEU LEU A . n A 1 111 VAL 111 111 111 VAL VAL A . n A 1 112 ASP 112 112 112 ASP ASP A . n A 1 113 THR 113 113 113 THR THR A . n A 1 114 GLU 114 114 114 GLU GLU A . n A 1 115 ASP 115 115 115 ASP ASP A . n A 1 116 THR 116 116 116 THR THR A . n A 1 117 ALA 117 117 117 ALA ALA A . n A 1 118 ILE 118 118 118 ILE ILE A . n A 1 119 LEU 119 119 119 LEU LEU A . n A 1 120 HIS 120 120 120 HIS HIS A . n A 1 121 GLY 121 121 121 GLY GLY A . n A 1 122 TRP 122 122 122 TRP TRP A . n A 1 123 GLU 123 123 123 GLU GLU A . n A 1 124 GLU 124 124 124 GLU GLU A . n A 1 125 ALA 125 125 125 ALA ALA A . n A 1 126 GLY 126 126 126 GLY GLY A . n A 1 127 ILE 127 127 127 ILE ILE A . n A 1 128 THR 128 128 128 THR THR A . n A 1 129 GLY 129 129 129 GLY GLY A . n A 1 130 LEU 130 130 130 LEU LEU A . n A 1 131 SER 131 131 131 SER SER A . n A 1 132 GLU 132 132 132 GLU GLU A . n A 1 133 ALA 133 133 133 ALA ALA A . n A 1 134 SER 134 134 134 SER SER A . n A 1 135 VAL 135 135 135 VAL VAL A . n A 1 136 HIS 136 136 136 HIS HIS A . n A 1 137 GLN 137 137 137 GLN GLN A . n A 1 138 PRO 138 138 138 PRO PRO A . n A 1 139 VAL 139 139 139 VAL VAL A . n A 1 140 GLN 140 140 140 GLN GLN A . n A 1 141 MET 141 141 141 MET MET A . n A 1 142 PRO 142 142 142 PRO PRO A . n A 1 143 ALA 143 143 143 ALA ALA A . n A 1 144 GLU 144 144 144 GLU GLU A . n A 1 145 LEU 145 145 145 LEU LEU A . n A 1 146 GLU 146 146 146 GLU GLU A . n A 1 147 GLN 147 147 147 GLN GLN A . n A 1 148 ILE 148 148 148 ILE ILE A . n A 1 149 ASP 149 149 149 ASP ASP A . n A 1 150 ASP 150 150 150 ASP ASP A . n A 1 151 ALA 151 151 151 ALA ALA A . n A 1 152 VAL 152 152 152 VAL VAL A . n A 1 153 SER 153 153 153 SER SER A . n A 1 154 GLY 154 154 154 GLY GLY A . n A 1 155 ALA 155 155 155 ALA ALA A . n A 1 156 CYS 156 156 156 CYS CYS A . n A 1 157 ASN 157 157 157 ASN ASN A . n A 1 158 VAL 158 158 158 VAL VAL A . n A 1 159 LEU 159 159 159 LEU LEU A . n A 1 160 ARG 160 160 160 ARG ARG A . n A 1 161 LEU 161 161 161 LEU LEU A . n A 1 162 ALA 162 162 162 ALA ALA A . n A 1 163 ASP 163 163 163 ASP ASP A . n A 1 164 VAL 164 164 164 VAL VAL A . n A 1 165 GLU 165 165 165 GLU GLU A . n A 1 166 GLY 166 166 166 GLY GLY A . n A 1 167 PRO 167 167 167 PRO PRO A . n A 1 168 TYR 168 168 168 TYR TYR A . n A 1 169 ASP 169 169 169 ASP ASP A . n A 1 170 LEU 170 170 170 LEU LEU A . n A 1 171 VAL 171 171 171 VAL VAL A . n A 1 172 LEU 172 172 172 LEU LEU A . n A 1 173 PRO 173 173 173 PRO PRO A . n A 1 174 GLN 174 174 174 GLN GLN A . n A 1 175 GLN 175 175 175 GLN GLN A . n A 1 176 LEU 176 176 176 LEU LEU A . n A 1 177 TYR 177 177 177 TYR TYR A . n A 1 178 THR 178 178 178 THR THR A . n A 1 179 GLN 179 179 179 GLN GLN A . n A 1 180 VAL 180 180 180 VAL VAL A . n A 1 181 SER 181 181 181 SER SER A . n A 1 182 GLU 182 182 182 GLU GLU A . n A 1 183 THR 183 183 183 THR THR A . n A 1 184 THR 184 184 184 THR THR A . n A 1 185 ASP 185 185 185 ASP ASP A . n A 1 186 HIS 186 186 186 HIS HIS A . n A 1 187 GLY 187 187 187 GLY GLY A . n A 1 188 VAL 188 188 188 VAL VAL A . n A 1 189 PRO 189 189 189 PRO PRO A . n A 1 190 VAL 190 190 190 VAL VAL A . n A 1 191 VAL 191 191 191 VAL VAL A . n A 1 192 ASP 192 192 192 ASP ASP A . n A 1 193 HIS 193 193 193 HIS HIS A . n A 1 194 LEU 194 194 194 LEU LEU A . n A 1 195 THR 195 195 195 THR THR A . n A 1 196 GLN 196 196 196 GLN GLN A . n A 1 197 LEU 197 197 197 LEU LEU A . n A 1 198 LEU 198 198 198 LEU LEU A . n A 1 199 SER 199 199 199 SER SER A . n A 1 200 GLY 200 200 200 GLY GLY A . n A 1 201 GLY 201 201 201 GLY GLY A . n A 1 202 GLU 202 202 202 GLU GLU A . n A 1 203 VAL 203 203 203 VAL VAL A . n A 1 204 LEU 204 204 204 LEU LEU A . n A 1 205 TRP 205 205 205 TRP TRP A . n A 1 206 ALA 206 206 206 ALA ALA A . n A 1 207 PRO 207 207 207 PRO PRO A . n A 1 208 ALA 208 208 208 ALA ALA A . n A 1 209 ALA 209 209 209 ALA ALA A . n A 1 210 ARG 210 210 210 ARG ARG A . n A 1 211 CYS 211 211 211 CYS CYS A . n A 1 212 ALA 212 212 212 ALA ALA A . n A 1 213 LEU 213 213 213 LEU LEU A . n A 1 214 VAL 214 214 214 VAL VAL A . n A 1 215 VAL 215 215 215 VAL VAL A . n A 1 216 SER 216 216 216 SER SER A . n A 1 217 ARG 217 217 217 ARG ARG A . n A 1 218 ARG 218 218 218 ARG ARG A . n A 1 219 GLY 219 219 219 GLY GLY A . n A 1 220 GLY 220 220 220 GLY GLY A . n A 1 221 ASP 221 221 221 ASP ASP A . n A 1 222 SER 222 222 222 SER SER A . n A 1 223 CYS 223 223 223 CYS CYS A . n A 1 224 LEU 224 224 224 LEU LEU A . n A 1 225 PHE 225 225 225 PHE PHE A . n A 1 226 LEU 226 226 226 LEU LEU A . n A 1 227 GLY 227 227 227 GLY GLY A . n A 1 228 ARG 228 228 228 ARG ARG A . n A 1 229 ASP 229 229 229 ASP ASP A . n A 1 230 VAL 230 230 230 VAL VAL A . n A 1 231 SER 231 231 231 SER SER A . n A 1 232 ILE 232 232 232 ILE ILE A . n A 1 233 GLY 233 233 233 GLY GLY A . n A 1 234 TYR 234 234 234 TYR TYR A . n A 1 235 LEU 235 235 235 LEU LEU A . n A 1 236 SER 236 236 236 SER SER A . n A 1 237 HIS 237 237 237 HIS HIS A . n A 1 238 ASP 238 238 238 ASP ASP A . n A 1 239 ALA 239 239 239 ALA ALA A . n A 1 240 GLN 240 240 240 GLN GLN A . n A 1 241 THR 241 241 241 THR THR A . n A 1 242 VAL 242 242 242 VAL VAL A . n A 1 243 THR 243 243 243 THR THR A . n A 1 244 LEU 244 244 244 LEU LEU A . n A 1 245 TYR 245 245 245 TYR TYR A . n A 1 246 LEU 246 246 246 LEU LEU A . n A 1 247 GLU 247 247 247 GLU GLU A . n A 1 248 GLU 248 248 248 GLU GLU A . n A 1 249 SER 249 249 249 SER SER A . n A 1 250 PHE 250 250 250 PHE PHE A . n A 1 251 THR 251 251 251 THR THR A . n A 1 252 PHE 252 252 252 PHE PHE A . n A 1 253 ARG 253 253 253 ARG ARG A . n A 1 254 VAL 254 254 254 VAL VAL A . n A 1 255 HIS 255 255 255 HIS HIS A . n A 1 256 GLN 256 256 256 GLN GLN A . n A 1 257 PRO 257 257 257 PRO PRO A . n A 1 258 ASP 258 258 258 ASP ASP A . n A 1 259 ALA 259 259 259 ALA ALA A . n A 1 260 ALA 260 260 260 ALA ALA A . n A 1 261 VAL 261 261 261 VAL VAL A . n A 1 262 ALA 262 262 262 ALA ALA A . n A 1 263 LEU 263 263 263 LEU LEU A . n A 1 264 VAL 264 264 264 VAL VAL A . n # _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 8DNA _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 8DNA _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 8DNA _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 8DNA _struct.title 'Acidipropionibacterium acidipropionici encapsulin in a closed state at pH 3.0' _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 8DNA _struct_keywords.text 'Encapsulin, VIRUS LIKE PARTICLE' _struct_keywords.pdbx_keywords 'VIRUS LIKE PARTICLE' # _struct_asym.id A _struct_asym.pdbx_blank_PDB_chainid_flag N _struct_asym.pdbx_modified N _struct_asym.entity_id 1 _struct_asym.details ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code K7RV67_ACIA4 _struct_ref.pdbx_db_accession K7RV67 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MNNLHRELAPISEAAWKQIDDEARDTFSLRAAGRRVVDVPEPAGPTLGSVSLGHLETGSQTDGVQTSVYRVQPLVQVRVP FTVSRADIDDVERGAVDLTWDPVDDAVAKLVDTEDTAILHGWEEAGITGLSEASVHQPVQMPAELEQIDDAVSGACNVLR LADVEGPYDLVLPQQLYTQVSETTDHGVPVVDHLTQLLSGGEVLWAPAARCALVVSRRGGDSCLFLGRDVSIGYLSHDAQ TVTLYLEESFTFRVHQPDAAVALV ; _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 8DNA _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 264 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession K7RV67 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 264 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 264 # 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 icosahedral assembly' ? 60-meric 60 2 'icosahedral asymmetric unit' ? monomeric 1 3 'icosahedral pentamer' ? pentameric 5 4 'icosahedral 23 hexamer' ? hexameric 6 5 'icosahedral 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 '(1-60)' A 2 1 A 3 '(1-5)' A 4 '(1,2,6,10,23,24)' A 5 P A # loop_ _pdbx_struct_assembly_auth_evidence.id _pdbx_struct_assembly_auth_evidence.assembly_id _pdbx_struct_assembly_auth_evidence.experimental_support _pdbx_struct_assembly_auth_evidence.details 1 1 'electron microscopy' ? 2 1 'gel filtration' ? 3 1 'light scattering' ? # 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' ? ? -0.80901603 0.50000060 -0.30901854 107.98263 0.50000127 0.30901530 -0.80901686 0.00007 -0.30901745 -0.80901727 -0.49999927 282.70301 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' ? ? 0.30901699 0.80901624 -0.50000123 66.73714 -0.80901643 0.50000082 0.30901714 174.71969 0.50000090 0.30901767 0.80901617 -107.98300 3 'point symmetry operation' ? ? -0.80901699 0.49999933 -0.30901808 282.70275 -0.49999986 -0.30901485 0.80901791 174.71964 0.30901722 0.80901822 0.49999786 -107.98290 4 'point symmetry operation' ? ? -0.80901699 -0.49999985 0.30901724 349.43970 0.49999932 -0.30901486 0.80901823 -0.00008 -0.30901808 0.80901790 0.49999786 0.00017 5 'point symmetry operation' ? ? 0.30901699 -0.80901644 0.50000091 174.71979 0.80901623 0.50000081 0.30901767 -107.98276 -0.50000123 0.30901714 0.80901618 66.73727 6 'point symmetry operation' ? ? -0.80901643 0.50000092 0.30901701 174.71929 0.50000091 0.30901789 0.80901609 -107.98280 0.30901700 0.80901608 -0.50000146 66.73738 7 'point symmetry operation' ? ? -0.50000000 -0.30901484 0.80901782 174.71927 0.30901700 0.80901832 0.49999786 -107.98265 -0.80901698 0.49999919 -0.30901831 282.70299 8 'point symmetry operation' ? ? 0.49999923 -0.30901499 0.80901824 -0.00045 -0.30901823 0.80901776 0.49999800 0.00042 -0.80901699 -0.49999999 0.30901700 349.43994 9 'point symmetry operation' ? ? 0.80901632 0.50000067 0.30901768 -107.98316 -0.50000110 0.30901700 0.80901632 66.73747 0.30901699 -0.80901657 0.50000068 174.72004 10 'point symmetry operation' ? ? 0.00000015 1.00000000 -0.00000007 -0.00042 0.00000022 0.00000008 1.00000000 0.00017 0.99999999 -0.00000015 -0.00000023 0.00025 11 'point symmetry operation' ? ? -0.49999746 0.30901609 -0.80901892 349.43969 0.30901609 -0.80901909 -0.49999718 349.44048 -0.80901891 -0.49999717 0.30901655 349.43987 12 'point symmetry operation' ? ? -0.80901699 -0.49999890 -0.30901877 457.42278 0.50000192 -0.30901914 -0.80901500 282.70296 0.30901389 -0.80901685 0.50000214 174.72037 13 'point symmetry operation' ? ? -0.00000234 -1.00000000 0.00000007 349.44042 0.00000242 -0.00000008 -1.00000000 349.43980 0.99999999 -0.00000235 0.00000242 0.00017 14 'point symmetry operation' ? ? 0.80901575 -0.50000269 -0.30901592 174.72057 -0.50000009 -0.30901575 -0.80901741 457.42295 0.30902010 0.80901580 -0.50000000 66.73664 15 'point symmetry operation' ? ? 0.50000177 0.30901375 -0.80901715 174.72011 -0.30901914 -0.80901699 -0.49999867 457.42337 -0.80901507 0.50000201 -0.30901877 282.70224 16 'point symmetry operation' ? ? 0.30901388 -0.80901701 0.50000191 174.72026 -0.80901700 -0.49999880 -0.30901891 457.42319 0.50000191 -0.30901891 -0.80901508 282.70271 17 'point symmetry operation' ? ? 1.00000000 -0.00000249 0.00000218 0.00005 -0.00000249 -1.00000000 0.00000000 349.44087 0.00000220 0.00000000 -1.00000000 349.43960 18 'point symmetry operation' ? ? 0.30902010 0.80901566 -0.50000024 66.73652 0.80901566 -0.50000283 -0.30901590 174.72101 -0.50000022 -0.30901589 -0.80901727 457.42275 19 'point symmetry operation' ? ? -0.80901507 0.50000187 -0.30901900 282.70213 0.50000187 0.30901361 -0.80901714 174.72053 -0.30901900 -0.80901713 -0.49999854 457.42312 20 'point symmetry operation' ? ? -0.80901892 -0.49999731 0.30901631 349.43975 -0.49999731 0.30901610 -0.80901900 349.44008 0.30901631 -0.80901900 -0.49999718 349.44020 21 'point symmetry operation' ? ? -0.30901809 0.80901776 0.49999810 -0.00003 -0.80901691 -0.50000000 0.30901722 349.44012 0.49999945 -0.30901500 0.80901809 -0.00029 22 'point symmetry operation' ? ? -0.50000100 0.30901713 0.80901633 66.73702 0.30901713 -0.80901644 0.50000081 174.72019 0.80901631 0.50000081 0.30901744 -107.98296 23 'point symmetry operation' ? ? 0.00000015 0.00000023 1.00000001 -0.00025 1.00000000 0.00000007 -0.00000015 0.00042 -0.00000008 1.00000000 -0.00000022 -0.00017 24 'point symmetry operation' ? ? 0.50000077 0.30901791 0.80901618 -107.98320 0.30901686 0.80901622 -0.50000133 66.73759 -0.80901657 0.50000068 0.30901700 174.71954 25 'point symmetry operation' ? ? 0.30901699 0.80901823 0.49999800 -107.98307 -0.80901708 0.49999919 -0.30901809 282.70320 -0.49999986 -0.30901507 0.80901781 174.71947 26 'point symmetry operation' ? ? 0.80901824 0.49999813 0.30901676 -107.98289 0.49999909 -0.30901824 -0.80901709 282.70366 -0.30901521 0.80901767 -0.50000000 174.71932 27 'point symmetry operation' ? ? 0.00000234 1.00000000 -0.00000257 -0.00037 -0.00000022 -0.00000257 -1.00000000 349.44069 -0.99999999 0.00000235 0.00000023 349.43935 28 'point symmetry operation' ? ? -0.80901700 0.50000192 0.30901390 174.71976 -0.49999890 -0.30901913 -0.80901686 457.42324 -0.30901877 -0.80901499 0.50000214 282.70260 29 'point symmetry operation' ? ? -0.50000254 -0.30901576 0.80901590 174.72021 -0.30901576 -0.80901755 -0.49999987 457.42308 0.80901589 -0.49999987 0.30902009 66.73699 30 'point symmetry operation' ? ? 0.49999823 -0.30901810 0.80901767 0.00037 0.30901698 -0.80901700 -0.50000001 349.44045 0.80901809 0.49999931 -0.30901522 -0.00035 31 'point symmetry operation' ? ? -0.00000015 -1.00000000 0.00000257 349.43960 -0.00000242 0.00000257 1.00000000 0.00020 -0.99999999 0.00000015 -0.00000242 349.44019 32 'point symmetry operation' ? ? 0.80901767 -0.50000015 -0.30901499 174.71963 0.49999808 0.30901699 0.80901818 -107.98252 -0.30901832 -0.80901690 0.49999932 282.70334 33 'point symmetry operation' ? ? 0.50000077 0.30901686 -0.80901658 174.71965 0.30901790 0.80901623 0.50000068 -107.98294 0.80901617 -0.50000133 0.30901699 66.73773 34 'point symmetry operation' ? ? -0.50000000 0.30901701 -0.80901699 349.43964 -0.30901485 0.80901832 0.49999919 -0.00048 0.80901781 0.49999785 -0.30901832 0.00050 35 'point symmetry operation' ? ? -0.80901756 -0.49999990 -0.30901566 457.42251 -0.49999990 0.30902038 0.80901577 66.73677 -0.30901566 0.80901576 -0.50000282 174.72023 36 'point symmetry operation' ? ? -0.49999999 -0.30901589 -0.80901742 457.42255 0.30902024 0.80901567 -0.50000014 66.73688 0.80901575 -0.50000283 -0.30901568 174.72073 37 'point symmetry operation' ? ? -0.30901901 -0.80901699 -0.49999877 457.42296 -0.80901499 0.50000201 -0.30901899 282.70250 0.50000200 0.30901375 -0.80901700 174.72023 38 'point symmetry operation' ? ? 0.30901607 -0.80901901 -0.49999733 349.44008 -0.80901900 -0.49999717 0.30901633 349.44015 -0.49999731 0.30901632 -0.80901891 349.43980 39 'point symmetry operation' ? ? 0.50000177 -0.30901915 -0.80901509 282.70260 0.30901375 -0.80901700 0.50000201 174.72067 -0.80901713 -0.49999867 -0.30901877 457.42294 40 'point symmetry operation' ? ? 0.00000235 -0.00000023 -1.00000001 349.43943 1.00000000 -0.00000257 0.00000234 0.00045 -0.00000257 -1.00000000 0.00000022 349.44061 41 'point symmetry operation' ? ? -0.30901809 -0.80901691 0.49999947 282.70310 0.80901775 -0.50000000 -0.30901500 174.72000 0.49999808 0.30901721 0.80901809 -107.98277 42 'point symmetry operation' ? ? 0.80901632 -0.50000110 0.30901699 66.73749 0.50000067 0.30901699 -0.80901658 174.72005 0.30901768 0.80901631 0.50000068 -107.98314 43 'point symmetry operation' ? ? 0.80901767 0.49999809 -0.30901833 0.00030 -0.50000014 0.30901700 -0.80901691 349.44006 -0.30901499 0.80901818 0.49999932 -0.00068 44 'point symmetry operation' ? ? -0.30901590 0.80901576 -0.50000268 174.72006 -0.80901755 -0.50000000 -0.30901553 457.42291 -0.49999977 0.30902024 0.80901590 66.73652 45 'point symmetry operation' ? ? -1.00000000 0.00000000 -0.00000218 349.44000 0.00000000 -1.00000000 0.00000264 349.43997 -0.00000220 0.00000265 1.00000000 -0.00008 46 'point symmetry operation' ? ? -0.00000015 -0.00000242 -1.00000001 349.44025 -1.00000000 0.00000257 0.00000015 349.43955 0.00000257 1.00000000 -0.00000242 -0.00025 47 'point symmetry operation' ? ? -0.49999900 -0.30901900 -0.80901685 457.42282 -0.30901900 -0.80901490 0.50000215 282.70285 -0.80901685 0.50000215 0.30901390 174.71987 48 'point symmetry operation' ? ? -0.30901590 -0.80901756 -0.49999977 457.42269 0.80901575 -0.50000000 0.30902023 66.73724 -0.50000268 -0.30901553 0.80901590 174.72037 49 'point symmetry operation' ? ? 0.30901700 -0.80901708 -0.49999987 349.44003 0.80901823 0.49999918 -0.30901508 -0.00015 0.49999799 -0.30901810 0.80901781 0.00056 50 'point symmetry operation' ? ? 0.49999923 -0.30901823 -0.80901701 282.70321 -0.30901499 0.80901776 -0.49999999 174.71949 0.80901823 0.49999799 0.30901699 -107.98272 51 'point symmetry operation' ? ? -0.50000001 0.30902024 0.80901576 66.73641 -0.30901589 0.80901567 -0.50000282 174.72051 -0.80901741 -0.50000013 -0.30901567 457.42270 52 'point symmetry operation' ? ? -0.00000235 0.00000242 1.00000001 -0.00019 -1.00000000 -0.00000007 -0.00000234 349.44045 0.00000008 -1.00000000 0.00000242 349.43977 53 'point symmetry operation' ? ? 0.49999823 0.30901698 0.80901810 -107.98293 -0.30901810 -0.80901699 0.49999932 282.70355 0.80901766 -0.50000001 -0.30901522 174.71982 54 'point symmetry operation' ? ? 0.30901791 0.80901631 0.50000054 -107.98334 0.80901631 -0.50000120 0.30901685 66.73794 0.50000054 0.30901685 -0.80901672 174.71989 55 'point symmetry operation' ? ? -0.30901498 0.80901833 0.49999910 -0.00085 0.80901768 0.49999798 -0.30901846 0.00075 -0.50000013 0.30901677 -0.80901699 349.43988 56 'point symmetry operation' ? ? 0.80901824 0.49999908 -0.30901522 -0.00052 0.49999813 -0.30901824 0.80901768 0.00081 0.30901676 -0.80901708 -0.50000000 349.44027 57 'point symmetry operation' ? ? -0.30901498 0.80901768 -0.50000014 174.71912 0.80901832 0.49999799 0.30901677 -107.98247 0.49999909 -0.30901846 -0.80901700 282.70346 58 'point symmetry operation' ? ? -1.00000000 0.00000249 0.00000000 349.43918 0.00000249 1.00000000 -0.00000264 0.00003 0.00000000 -0.00000265 -1.00000000 349.44044 59 'point symmetry operation' ? ? -0.30901901 -0.80901499 0.50000201 282.70248 -0.80901699 0.50000202 0.30901376 174.72017 -0.49999876 -0.30901899 -0.80901699 457.42298 60 'point symmetry operation' ? ? 0.80901575 -0.50000010 0.30902010 66.73687 -0.50000268 -0.30901575 0.80901582 174.72065 -0.30901590 -0.80901741 -0.50000000 457.42288 # 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 5 ? ALA A 9 ? HIS A 5 ALA A 9 5 ? 5 HELX_P HELX_P2 AA2 SER A 12 ? ALA A 31 ? SER A 12 ALA A 31 1 ? 20 HELX_P HELX_P3 AA3 ALA A 32 ? VAL A 36 ? ALA A 32 VAL A 36 5 ? 5 HELX_P HELX_P4 AA4 ARG A 85 ? GLY A 94 ? ARG A 85 GLY A 94 1 ? 10 HELX_P HELX_P5 AA5 TRP A 100 ? HIS A 120 ? TRP A 100 HIS A 120 1 ? 21 HELX_P HELX_P6 AA6 GLN A 147 ? ALA A 162 ? GLN A 147 ALA A 162 1 ? 16 HELX_P HELX_P7 AA7 PRO A 173 ? THR A 183 ? PRO A 173 THR A 183 1 ? 11 HELX_P HELX_P8 AA8 PRO A 189 ? LEU A 198 ? PRO A 189 LEU A 198 1 ? 10 HELX_P HELX_P9 AA9 GLN A 256 ? ASP A 258 ? GLN A 256 ASP A 258 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 2 ? AA2 ? 2 ? AA3 ? 3 ? AA4 ? 3 ? AA5 ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? anti-parallel AA2 1 2 ? anti-parallel AA3 1 2 ? anti-parallel AA3 2 3 ? anti-parallel AA4 1 2 ? anti-parallel AA4 2 3 ? anti-parallel AA5 1 2 ? parallel AA5 2 3 ? anti-parallel AA5 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 SER A 49 ? LEU A 55 ? SER A 49 LEU A 55 AA1 2 TYR A 69 ? PRO A 73 ? TYR A 69 PRO A 73 AA2 1 SER A 59 ? THR A 61 ? SER A 59 THR A 61 AA2 2 VAL A 64 ? THR A 66 ? VAL A 64 THR A 66 AA3 1 VAL A 75 ? SER A 84 ? VAL A 75 SER A 84 AA3 2 THR A 241 ? VAL A 254 ? THR A 241 VAL A 254 AA3 3 SER A 222 ? LEU A 226 ? SER A 222 LEU A 226 AA4 1 VAL A 75 ? SER A 84 ? VAL A 75 SER A 84 AA4 2 THR A 241 ? VAL A 254 ? THR A 241 VAL A 254 AA4 3 SER A 231 ? HIS A 237 ? SER A 231 HIS A 237 AA5 1 VAL A 203 ? TRP A 205 ? VAL A 203 TRP A 205 AA5 2 TYR A 168 ? LEU A 172 ? TYR A 168 LEU A 172 AA5 3 ALA A 212 ? SER A 216 ? ALA A 212 SER A 216 AA5 4 ALA A 260 ? LEU A 263 ? ALA A 260 LEU A 263 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N VAL A 50 ? N VAL A 50 O GLN A 72 ? O GLN A 72 AA2 1 2 N SER A 59 ? N SER A 59 O THR A 66 ? O THR A 66 AA3 1 2 N VAL A 83 ? N VAL A 83 O VAL A 242 ? O VAL A 242 AA3 2 3 O ARG A 253 ? O ARG A 253 N CYS A 223 ? N CYS A 223 AA4 1 2 N VAL A 83 ? N VAL A 83 O VAL A 242 ? O VAL A 242 AA4 2 3 O THR A 243 ? O THR A 243 N SER A 236 ? N SER A 236 AA5 1 2 O LEU A 204 ? O LEU A 204 N LEU A 172 ? N LEU A 172 AA5 2 3 N ASP A 169 ? N ASP A 169 O VAL A 215 ? O VAL A 215 AA5 3 4 N VAL A 214 ? N VAL A 214 O VAL A 261 ? O VAL A 261 # 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 ASP A 62 ? ? 54.12 -142.91 2 1 GLU A 123 ? ? 72.65 -8.98 3 1 GLU A 144 ? ? 68.30 -5.89 4 1 LEU A 145 ? ? 67.34 -4.92 5 1 GLU A 165 ? ? 55.05 -168.47 6 1 ASP A 185 ? ? 57.33 -132.48 # _pdbx_point_symmetry.entry_id 8DNA _pdbx_point_symmetry.Schoenflies_symbol I # _em_3d_fitting.entry_id 8DNA _em_3d_fitting.id 1 _em_3d_fitting.details ;A starting model was created using RosettaFold. The starting model was placed in the map manually using UCSF Chimera. The model was then further refined using Coot and Phenix Real Space Refine. ; _em_3d_fitting.overall_b_value 28.55 _em_3d_fitting.ref_protocol 'AB INITIO MODEL' _em_3d_fitting.ref_space REAL _em_3d_fitting.target_criteria 'Correlation coefficient' _em_3d_fitting.method ? # _em_3d_reconstruction.entry_id 8DNA _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 47164 _em_3d_reconstruction.resolution 2.77 _em_3d_reconstruction.resolution_method 'FSC 0.143 CUT-OFF' _em_3d_reconstruction.symmetry_type POINT _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 3.0 _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 'Acidipropionibacterium acidipropionici encapsulin in a closed state at pH 3.0' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type COMPLEX _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 8DNA _em_image_scans.id 1 _em_image_scans.dimension_height 3710 _em_image_scans.dimension_width 3838 _em_image_scans.frames_per_image 40 _em_image_scans.image_recording_id 1 _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.used_frames_per_image ? _em_image_scans.citation_id ? _em_image_scans.number_digital_images ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.details ? # _em_imaging.id 1 _em_imaging.entry_id 8DNA _em_imaging.accelerating_voltage 200 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter 70 _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen NITROGEN _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI TALOS ARCTICA' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs 2.7 _em_imaging.nominal_defocus_max 1800 _em_imaging.nominal_defocus_min 1000 _em_imaging.nominal_magnification 45000 _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_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details 'The grid was glow discharged for 60 seconds at 5 mA.' _em_sample_support.grid_material COPPER _em_sample_support.grid_mesh_size 200 _em_sample_support.grid_type 'Quantifoil R1.2/1.3' _em_sample_support.method ? _em_sample_support.film_material ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature 295 _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity 100 _em_vitrification.instrument 'FEI VITROBOT MARK IV' _em_vitrification.entry_id 8DNA _em_vitrification.citation_id ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 8DNA _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.reconstruction_method 'SINGLE PARTICLE' _em_experiment.entity_assembly_id 1 # _em_single_particle_entity.entry_id 8DNA _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry I # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal ALA N N N N 1 ALA CA C N S 2 ALA C C N N 3 ALA O O N N 4 ALA CB C N N 5 ALA OXT O N N 6 ALA H H N N 7 ALA H2 H N N 8 ALA HA H N N 9 ALA HB1 H N N 10 ALA HB2 H N N 11 ALA HB3 H N N 12 ALA HXT H N N 13 ARG N N N N 14 ARG CA C N S 15 ARG C C N N 16 ARG O O N N 17 ARG CB C N N 18 ARG CG C N N 19 ARG CD C N N 20 ARG NE N N N 21 ARG CZ C N N 22 ARG NH1 N N N 23 ARG NH2 N N N 24 ARG OXT O N N 25 ARG H H N N 26 ARG H2 H N N 27 ARG HA H N N 28 ARG HB2 H N N 29 ARG HB3 H N N 30 ARG HG2 H N N 31 ARG HG3 H N N 32 ARG HD2 H N N 33 ARG HD3 H N N 34 ARG HE H N N 35 ARG HH11 H N N 36 ARG HH12 H N N 37 ARG HH21 H N N 38 ARG HH22 H N N 39 ARG HXT H N N 40 ASN N N N N 41 ASN CA C N S 42 ASN C C N N 43 ASN O O N N 44 ASN CB C N N 45 ASN CG C N N 46 ASN OD1 O N N 47 ASN ND2 N N N 48 ASN OXT O N N 49 ASN H H N N 50 ASN H2 H N N 51 ASN HA H N N 52 ASN HB2 H N N 53 ASN HB3 H N N 54 ASN HD21 H N N 55 ASN HD22 H N N 56 ASN HXT H N N 57 ASP N N N N 58 ASP CA C N S 59 ASP C C N N 60 ASP O O N N 61 ASP CB C N N 62 ASP CG C N N 63 ASP OD1 O N N 64 ASP OD2 O N N 65 ASP OXT O N N 66 ASP H H N N 67 ASP H2 H N N 68 ASP HA H N N 69 ASP HB2 H N N 70 ASP HB3 H N N 71 ASP HD2 H N N 72 ASP HXT H N N 73 CYS N N N N 74 CYS CA C N R 75 CYS C C N N 76 CYS O O N N 77 CYS CB C N N 78 CYS SG S N N 79 CYS OXT O N N 80 CYS H H N N 81 CYS H2 H N N 82 CYS HA H N N 83 CYS HB2 H N N 84 CYS HB3 H N N 85 CYS HG H N N 86 CYS HXT H N N 87 GLN N N N N 88 GLN CA C N S 89 GLN C C N N 90 GLN O O N N 91 GLN CB C N N 92 GLN CG C N N 93 GLN CD C N N 94 GLN OE1 O N N 95 GLN NE2 N N N 96 GLN OXT O N N 97 GLN H H N N 98 GLN H2 H N N 99 GLN HA H N N 100 GLN HB2 H N N 101 GLN HB3 H N N 102 GLN HG2 H N N 103 GLN HG3 H N N 104 GLN HE21 H N N 105 GLN HE22 H N N 106 GLN HXT H N N 107 GLU N N N N 108 GLU CA C N S 109 GLU C C N N 110 GLU O O N N 111 GLU CB C N N 112 GLU CG C N N 113 GLU CD C N N 114 GLU OE1 O N N 115 GLU OE2 O N N 116 GLU OXT O N N 117 GLU H H N N 118 GLU H2 H N N 119 GLU HA H N N 120 GLU HB2 H N N 121 GLU HB3 H N N 122 GLU HG2 H N N 123 GLU HG3 H N N 124 GLU HE2 H N N 125 GLU HXT H N N 126 GLY N N N N 127 GLY CA C N N 128 GLY C C N N 129 GLY O O N N 130 GLY OXT O N N 131 GLY H H N N 132 GLY H2 H N N 133 GLY HA2 H N N 134 GLY HA3 H N N 135 GLY HXT H N N 136 HIS N N N N 137 HIS CA C N S 138 HIS C C N N 139 HIS O O N N 140 HIS CB C N N 141 HIS CG C Y N 142 HIS ND1 N Y N 143 HIS CD2 C Y N 144 HIS CE1 C Y N 145 HIS NE2 N Y N 146 HIS OXT O N N 147 HIS H H N N 148 HIS H2 H N N 149 HIS HA H N N 150 HIS HB2 H N N 151 HIS HB3 H N N 152 HIS HD1 H N N 153 HIS HD2 H N N 154 HIS HE1 H N N 155 HIS HE2 H N N 156 HIS HXT H N N 157 ILE N N N N 158 ILE CA C N S 159 ILE C C N N 160 ILE O O N N 161 ILE CB C N S 162 ILE CG1 C N N 163 ILE CG2 C N N 164 ILE CD1 C N N 165 ILE OXT O N N 166 ILE H H N N 167 ILE H2 H N N 168 ILE HA H N N 169 ILE HB H N N 170 ILE HG12 H N N 171 ILE HG13 H N N 172 ILE HG21 H N N 173 ILE HG22 H N N 174 ILE HG23 H N N 175 ILE HD11 H N N 176 ILE HD12 H N N 177 ILE HD13 H N N 178 ILE HXT H N N 179 LEU N N N N 180 LEU CA C N S 181 LEU C C N N 182 LEU O O N N 183 LEU CB C N N 184 LEU CG C N N 185 LEU CD1 C N N 186 LEU CD2 C N N 187 LEU OXT O N N 188 LEU H H N N 189 LEU H2 H N N 190 LEU HA H N N 191 LEU HB2 H N N 192 LEU HB3 H N N 193 LEU HG H N N 194 LEU HD11 H N N 195 LEU HD12 H N N 196 LEU HD13 H N N 197 LEU HD21 H N N 198 LEU HD22 H N N 199 LEU HD23 H N N 200 LEU HXT H N N 201 LYS N N N N 202 LYS CA C N S 203 LYS C C N N 204 LYS O O N N 205 LYS CB C N N 206 LYS CG C N N 207 LYS CD C N N 208 LYS CE C N N 209 LYS NZ N N N 210 LYS OXT O N N 211 LYS H H N N 212 LYS H2 H N N 213 LYS HA H N N 214 LYS HB2 H N N 215 LYS HB3 H N N 216 LYS HG2 H N N 217 LYS HG3 H N N 218 LYS HD2 H N N 219 LYS HD3 H N N 220 LYS HE2 H N N 221 LYS HE3 H N N 222 LYS HZ1 H N N 223 LYS HZ2 H N N 224 LYS HZ3 H N N 225 LYS HXT H N N 226 MET N N N N 227 MET CA C N S 228 MET C C N N 229 MET O O N N 230 MET CB C N N 231 MET CG C N N 232 MET SD S N N 233 MET CE C N N 234 MET OXT O N N 235 MET H H N N 236 MET H2 H N N 237 MET HA H N N 238 MET HB2 H N N 239 MET HB3 H N N 240 MET HG2 H N N 241 MET HG3 H N N 242 MET HE1 H N N 243 MET HE2 H N N 244 MET HE3 H N N 245 MET HXT H N N 246 PHE N N N N 247 PHE CA C N S 248 PHE C C N N 249 PHE O O N N 250 PHE CB C N N 251 PHE CG C Y N 252 PHE CD1 C Y N 253 PHE CD2 C Y N 254 PHE CE1 C Y N 255 PHE CE2 C Y N 256 PHE CZ C Y N 257 PHE OXT O N N 258 PHE H H N N 259 PHE H2 H N N 260 PHE HA H N N 261 PHE HB2 H N N 262 PHE HB3 H N N 263 PHE HD1 H N N 264 PHE HD2 H N N 265 PHE HE1 H N N 266 PHE HE2 H N N 267 PHE HZ H N N 268 PHE HXT H N N 269 PRO N N N N 270 PRO CA C N S 271 PRO C C N N 272 PRO O O N N 273 PRO CB C N N 274 PRO CG C N N 275 PRO CD C N N 276 PRO OXT O N N 277 PRO H H N N 278 PRO HA H N N 279 PRO HB2 H N N 280 PRO HB3 H N N 281 PRO HG2 H N N 282 PRO HG3 H N N 283 PRO HD2 H N N 284 PRO HD3 H N N 285 PRO HXT H N N 286 SER N N N N 287 SER CA C N S 288 SER C C N N 289 SER O O N N 290 SER CB C N N 291 SER OG O N N 292 SER OXT O N N 293 SER H H N N 294 SER H2 H N N 295 SER HA H N N 296 SER HB2 H N N 297 SER HB3 H N N 298 SER HG H N N 299 SER HXT H N N 300 THR N N N N 301 THR CA C N S 302 THR C C N N 303 THR O O N N 304 THR CB C N R 305 THR OG1 O N N 306 THR CG2 C N N 307 THR OXT O N N 308 THR H H N N 309 THR H2 H N N 310 THR HA H N N 311 THR HB H N N 312 THR HG1 H N N 313 THR HG21 H N N 314 THR HG22 H N N 315 THR HG23 H N N 316 THR HXT H N N 317 TRP N N N N 318 TRP CA C N S 319 TRP C C N N 320 TRP O O N N 321 TRP CB C N N 322 TRP CG C Y N 323 TRP CD1 C Y N 324 TRP CD2 C Y N 325 TRP NE1 N Y N 326 TRP CE2 C Y N 327 TRP CE3 C Y N 328 TRP CZ2 C Y N 329 TRP CZ3 C Y N 330 TRP CH2 C Y N 331 TRP OXT O N N 332 TRP H H N N 333 TRP H2 H N N 334 TRP HA H N N 335 TRP HB2 H N N 336 TRP HB3 H N N 337 TRP HD1 H N N 338 TRP HE1 H N N 339 TRP HE3 H N N 340 TRP HZ2 H N N 341 TRP HZ3 H N N 342 TRP HH2 H N N 343 TRP HXT H N N 344 TYR N N N N 345 TYR CA C N S 346 TYR C C N N 347 TYR O O N N 348 TYR CB C N N 349 TYR CG C Y N 350 TYR CD1 C Y N 351 TYR CD2 C Y N 352 TYR CE1 C Y N 353 TYR CE2 C Y N 354 TYR CZ C Y N 355 TYR OH O N N 356 TYR OXT O N N 357 TYR H H N N 358 TYR H2 H N N 359 TYR HA H N N 360 TYR HB2 H N N 361 TYR HB3 H N N 362 TYR HD1 H N N 363 TYR HD2 H N N 364 TYR HE1 H N N 365 TYR HE2 H N N 366 TYR HH H N N 367 TYR HXT H N N 368 VAL N N N N 369 VAL CA C N S 370 VAL C C N N 371 VAL O O N N 372 VAL CB C N N 373 VAL CG1 C N N 374 VAL CG2 C N N 375 VAL OXT O N N 376 VAL H H N N 377 VAL H2 H N N 378 VAL HA H N N 379 VAL HB H N N 380 VAL HG11 H N N 381 VAL HG12 H N N 382 VAL HG13 H N N 383 VAL HG21 H N N 384 VAL HG22 H N N 385 VAL HG23 H N N 386 VAL HXT H N N 387 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal ALA N CA sing N N 1 ALA N H sing N N 2 ALA N H2 sing N N 3 ALA CA C sing N N 4 ALA CA CB sing N N 5 ALA CA HA sing N N 6 ALA C O doub N N 7 ALA C OXT sing N N 8 ALA CB HB1 sing N N 9 ALA CB HB2 sing N N 10 ALA CB HB3 sing N N 11 ALA OXT HXT sing N N 12 ARG N CA sing N N 13 ARG N H sing N N 14 ARG N H2 sing N N 15 ARG CA C sing N N 16 ARG CA CB sing N N 17 ARG CA HA sing N N 18 ARG C O doub N N 19 ARG C OXT sing N N 20 ARG CB CG sing N N 21 ARG CB HB2 sing N N 22 ARG CB HB3 sing N N 23 ARG CG CD sing N N 24 ARG CG HG2 sing N N 25 ARG CG HG3 sing N N 26 ARG CD NE sing N N 27 ARG CD HD2 sing N N 28 ARG CD HD3 sing N N 29 ARG NE CZ sing N N 30 ARG NE HE sing N N 31 ARG CZ NH1 sing N N 32 ARG CZ NH2 doub N N 33 ARG NH1 HH11 sing N N 34 ARG NH1 HH12 sing N N 35 ARG NH2 HH21 sing N N 36 ARG NH2 HH22 sing N N 37 ARG OXT HXT sing N N 38 ASN N CA sing N N 39 ASN N H sing N N 40 ASN N H2 sing N N 41 ASN CA C sing N N 42 ASN CA CB sing N N 43 ASN CA HA sing N N 44 ASN C O doub N N 45 ASN C OXT sing N N 46 ASN CB CG sing N N 47 ASN CB HB2 sing N N 48 ASN CB HB3 sing N N 49 ASN CG OD1 doub N N 50 ASN CG ND2 sing N N 51 ASN ND2 HD21 sing N N 52 ASN ND2 HD22 sing N N 53 ASN OXT HXT sing N N 54 ASP N CA sing N N 55 ASP N H sing N N 56 ASP N H2 sing N N 57 ASP CA C sing N N 58 ASP CA CB sing N N 59 ASP CA HA sing N N 60 ASP C O doub N N 61 ASP C OXT sing N N 62 ASP CB CG sing N N 63 ASP CB HB2 sing N N 64 ASP CB HB3 sing N N 65 ASP CG OD1 doub N N 66 ASP CG OD2 sing N N 67 ASP OD2 HD2 sing N N 68 ASP OXT HXT sing N N 69 CYS N CA sing N N 70 CYS N H sing N N 71 CYS N H2 sing N N 72 CYS CA C sing N N 73 CYS CA CB sing N N 74 CYS CA HA sing N N 75 CYS C O doub N N 76 CYS C OXT sing N N 77 CYS CB SG sing N N 78 CYS CB HB2 sing N N 79 CYS CB HB3 sing N N 80 CYS SG HG sing N N 81 CYS OXT HXT sing N N 82 GLN N CA sing N N 83 GLN N H sing N N 84 GLN N H2 sing N N 85 GLN CA C sing N N 86 GLN CA CB sing N N 87 GLN CA HA sing N N 88 GLN C O doub N N 89 GLN C OXT sing N N 90 GLN CB CG sing N N 91 GLN CB HB2 sing N N 92 GLN CB HB3 sing N N 93 GLN CG CD sing N N 94 GLN CG HG2 sing N N 95 GLN CG HG3 sing N N 96 GLN CD OE1 doub N N 97 GLN CD NE2 sing N N 98 GLN NE2 HE21 sing N N 99 GLN NE2 HE22 sing N N 100 GLN OXT HXT sing N N 101 GLU N CA sing N N 102 GLU N H sing N N 103 GLU N H2 sing N N 104 GLU CA C sing N N 105 GLU CA CB sing N N 106 GLU CA HA sing N N 107 GLU C O doub N N 108 GLU C OXT sing N N 109 GLU CB CG sing N N 110 GLU CB HB2 sing N N 111 GLU CB HB3 sing N N 112 GLU CG CD sing N N 113 GLU CG HG2 sing N N 114 GLU CG HG3 sing N N 115 GLU CD OE1 doub N N 116 GLU CD OE2 sing N N 117 GLU OE2 HE2 sing N N 118 GLU OXT HXT sing N N 119 GLY N CA sing N N 120 GLY N H sing N N 121 GLY N H2 sing N N 122 GLY CA C sing N N 123 GLY CA HA2 sing N N 124 GLY CA HA3 sing N N 125 GLY C O doub N N 126 GLY C OXT sing N N 127 GLY OXT HXT sing N N 128 HIS N CA sing N N 129 HIS N H sing N N 130 HIS N H2 sing N N 131 HIS CA C sing N N 132 HIS CA CB sing N N 133 HIS CA HA sing N N 134 HIS C O doub N N 135 HIS C OXT sing N N 136 HIS CB CG sing N N 137 HIS CB HB2 sing N N 138 HIS CB HB3 sing N N 139 HIS CG ND1 sing Y N 140 HIS CG CD2 doub Y N 141 HIS ND1 CE1 doub Y N 142 HIS ND1 HD1 sing N N 143 HIS CD2 NE2 sing Y N 144 HIS CD2 HD2 sing N N 145 HIS CE1 NE2 sing Y N 146 HIS CE1 HE1 sing N N 147 HIS NE2 HE2 sing N N 148 HIS OXT HXT sing N N 149 ILE N CA sing N N 150 ILE N H sing N N 151 ILE N H2 sing N N 152 ILE CA C sing N N 153 ILE CA CB sing N N 154 ILE CA HA sing N N 155 ILE C O doub N N 156 ILE C OXT sing N N 157 ILE CB CG1 sing N N 158 ILE CB CG2 sing N N 159 ILE CB HB sing N N 160 ILE CG1 CD1 sing N N 161 ILE CG1 HG12 sing N N 162 ILE CG1 HG13 sing N N 163 ILE CG2 HG21 sing N N 164 ILE CG2 HG22 sing N N 165 ILE CG2 HG23 sing N N 166 ILE CD1 HD11 sing N N 167 ILE CD1 HD12 sing N N 168 ILE CD1 HD13 sing N N 169 ILE OXT HXT sing N N 170 LEU N CA sing N N 171 LEU N H sing N N 172 LEU N H2 sing N N 173 LEU CA C sing N N 174 LEU CA CB sing N N 175 LEU CA HA sing N N 176 LEU C O doub N N 177 LEU C OXT sing N N 178 LEU CB CG sing N N 179 LEU CB HB2 sing N N 180 LEU CB HB3 sing N N 181 LEU CG CD1 sing N N 182 LEU CG CD2 sing N N 183 LEU CG HG sing N N 184 LEU CD1 HD11 sing N N 185 LEU CD1 HD12 sing N N 186 LEU CD1 HD13 sing N N 187 LEU CD2 HD21 sing N N 188 LEU CD2 HD22 sing N N 189 LEU CD2 HD23 sing N N 190 LEU OXT HXT sing N N 191 LYS N CA sing N N 192 LYS N H sing N N 193 LYS N H2 sing N N 194 LYS CA C sing N N 195 LYS CA CB sing N N 196 LYS CA HA sing N N 197 LYS C O doub N N 198 LYS C OXT sing N N 199 LYS CB CG sing N N 200 LYS CB HB2 sing N N 201 LYS CB HB3 sing N N 202 LYS CG CD sing N N 203 LYS CG HG2 sing N N 204 LYS CG HG3 sing N N 205 LYS CD CE sing N N 206 LYS CD HD2 sing N N 207 LYS CD HD3 sing N N 208 LYS CE NZ sing N N 209 LYS CE HE2 sing N N 210 LYS CE HE3 sing N N 211 LYS NZ HZ1 sing N N 212 LYS NZ HZ2 sing N N 213 LYS NZ HZ3 sing N N 214 LYS OXT HXT sing N N 215 MET N CA sing N N 216 MET N H sing N N 217 MET N H2 sing N N 218 MET CA C sing N N 219 MET CA CB sing N N 220 MET CA HA sing N N 221 MET C O doub N N 222 MET C OXT sing N N 223 MET CB CG sing N N 224 MET CB HB2 sing N N 225 MET CB HB3 sing N N 226 MET CG SD sing N N 227 MET CG HG2 sing N N 228 MET CG HG3 sing N N 229 MET SD CE sing N N 230 MET CE HE1 sing N N 231 MET CE HE2 sing N N 232 MET CE HE3 sing N N 233 MET OXT HXT sing N N 234 PHE N CA sing N N 235 PHE N H sing N N 236 PHE N H2 sing N N 237 PHE CA C sing N N 238 PHE CA CB sing N N 239 PHE CA HA sing N N 240 PHE C O doub N N 241 PHE C OXT sing N N 242 PHE CB CG sing N N 243 PHE CB HB2 sing N N 244 PHE CB HB3 sing N N 245 PHE CG CD1 doub Y N 246 PHE CG CD2 sing Y N 247 PHE CD1 CE1 sing Y N 248 PHE CD1 HD1 sing N N 249 PHE CD2 CE2 doub Y N 250 PHE CD2 HD2 sing N N 251 PHE CE1 CZ doub Y N 252 PHE CE1 HE1 sing N N 253 PHE CE2 CZ sing Y N 254 PHE CE2 HE2 sing N N 255 PHE CZ HZ sing N N 256 PHE OXT HXT sing N N 257 PRO N CA sing N N 258 PRO N CD sing N N 259 PRO N H sing N N 260 PRO CA C sing N N 261 PRO CA CB sing N N 262 PRO CA HA sing N N 263 PRO C O doub N N 264 PRO C OXT sing N N 265 PRO CB CG sing N N 266 PRO CB HB2 sing N N 267 PRO CB HB3 sing N N 268 PRO CG CD sing N N 269 PRO CG HG2 sing N N 270 PRO CG HG3 sing N N 271 PRO CD HD2 sing N N 272 PRO CD HD3 sing N N 273 PRO OXT HXT sing N N 274 SER N CA sing N N 275 SER N H sing N N 276 SER N H2 sing N N 277 SER CA C sing N N 278 SER CA CB sing N N 279 SER CA HA sing N N 280 SER C O doub N N 281 SER C OXT sing N N 282 SER CB OG sing N N 283 SER CB HB2 sing N N 284 SER CB HB3 sing N N 285 SER OG HG sing N N 286 SER OXT HXT sing N N 287 THR N CA sing N N 288 THR N H sing N N 289 THR N H2 sing N N 290 THR CA C sing N N 291 THR CA CB sing N N 292 THR CA HA sing N N 293 THR C O doub N N 294 THR C OXT sing N N 295 THR CB OG1 sing N N 296 THR CB CG2 sing N N 297 THR CB HB sing N N 298 THR OG1 HG1 sing N N 299 THR CG2 HG21 sing N N 300 THR CG2 HG22 sing N N 301 THR CG2 HG23 sing N N 302 THR OXT HXT sing N N 303 TRP N CA sing N N 304 TRP N H sing N N 305 TRP N H2 sing N N 306 TRP CA C sing N N 307 TRP CA CB sing N N 308 TRP CA HA sing N N 309 TRP C O doub N N 310 TRP C OXT sing N N 311 TRP CB CG sing N N 312 TRP CB HB2 sing N N 313 TRP CB HB3 sing N N 314 TRP CG CD1 doub Y N 315 TRP CG CD2 sing Y N 316 TRP CD1 NE1 sing Y N 317 TRP CD1 HD1 sing N N 318 TRP CD2 CE2 doub Y N 319 TRP CD2 CE3 sing Y N 320 TRP NE1 CE2 sing Y N 321 TRP NE1 HE1 sing N N 322 TRP CE2 CZ2 sing Y N 323 TRP CE3 CZ3 doub Y N 324 TRP CE3 HE3 sing N N 325 TRP CZ2 CH2 doub Y N 326 TRP CZ2 HZ2 sing N N 327 TRP CZ3 CH2 sing Y N 328 TRP CZ3 HZ3 sing N N 329 TRP CH2 HH2 sing N N 330 TRP OXT HXT sing N N 331 TYR N CA sing N N 332 TYR N H sing N N 333 TYR N H2 sing N N 334 TYR CA C sing N N 335 TYR CA CB sing N N 336 TYR CA HA sing N N 337 TYR C O doub N N 338 TYR C OXT sing N N 339 TYR CB CG sing N N 340 TYR CB HB2 sing N N 341 TYR CB HB3 sing N N 342 TYR CG CD1 doub Y N 343 TYR CG CD2 sing Y N 344 TYR CD1 CE1 sing Y N 345 TYR CD1 HD1 sing N N 346 TYR CD2 CE2 doub Y N 347 TYR CD2 HD2 sing N N 348 TYR CE1 CZ doub Y N 349 TYR CE1 HE1 sing N N 350 TYR CE2 CZ sing Y N 351 TYR CE2 HE2 sing N N 352 TYR CZ OH sing N N 353 TYR OH HH sing N N 354 TYR OXT HXT sing N N 355 VAL N CA sing N N 356 VAL N H sing N N 357 VAL N H2 sing N N 358 VAL CA C sing N N 359 VAL CA CB sing N N 360 VAL CA HA sing N N 361 VAL C O doub N N 362 VAL C OXT sing N N 363 VAL CB CG1 sing N N 364 VAL CB CG2 sing N N 365 VAL CB HB sing N N 366 VAL CG1 HG11 sing N N 367 VAL CG1 HG12 sing N N 368 VAL CG1 HG13 sing N N 369 VAL CG2 HG21 sing N N 370 VAL CG2 HG22 sing N N 371 VAL CG2 HG23 sing N N 372 VAL OXT HXT sing N N 373 # loop_ _em_buffer_component.buffer_id _em_buffer_component.id _em_buffer_component.concentration _em_buffer_component.concentration_units _em_buffer_component.formula _em_buffer_component.name 1 1 150 mM NaCl 'sodium chloride' 1 2 50 mM NaH2PO4 'monosodium phosphate' # _em_ctf_correction.id 1 _em_ctf_correction.em_image_processing_id 1 _em_ctf_correction.type 'PHASE FLIPPING AND AMPLITUDE CORRECTION' _em_ctf_correction.details ? # _em_entity_assembly_molwt.entity_assembly_id 1 _em_entity_assembly_molwt.id 1 _em_entity_assembly_molwt.experimental_flag YES _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 1.71 # _em_entity_assembly_naturalsource.id 2 _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 1171373 _em_entity_assembly_naturalsource.organ ? _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Acidipropionibacterium acidipropionici ATCC 4875' _em_entity_assembly_naturalsource.strain ? _em_entity_assembly_naturalsource.tissue ? # _em_entity_assembly_recombinant.id 2 _em_entity_assembly_recombinant.entity_assembly_id 1 _em_entity_assembly_recombinant.cell ? _em_entity_assembly_recombinant.ncbi_tax_id 469008 _em_entity_assembly_recombinant.organism 'Escherichia coli BL21(DE3)' _em_entity_assembly_recombinant.plasmid ? _em_entity_assembly_recombinant.strain ? # _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 43 _em_image_recording.average_exposure_time 8 _em_image_recording.details ? _em_image_recording.detector_mode COUNTING _em_image_recording.film_or_detector_model 'GATAN K2 SUMMIT (4k x 4k)' _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged 1 _em_image_recording.num_real_images 1357 _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' ? cryoSPARC 3.3.1 1 ? ? 2 'IMAGE ACQUISITION' ? Leginon ? ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? cryoSPARC 3.3.1 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? PHENIX 1.19.2-4158 ? 1 ? 8 'MODEL FITTING' ? 'UCSF Chimera' 1.16 ? 1 ? 9 OTHER ? ? ? ? ? ? 10 'INITIAL EULER ASSIGNMENT' ? cryoSPARC 3.3.1 1 ? ? 11 'FINAL EULER ASSIGNMENT' ? cryoSPARC 3.3.1 1 ? ? 12 CLASSIFICATION ? ? ? 1 ? ? 13 RECONSTRUCTION ? cryoSPARC 3.3.1 1 ? ? 14 'MODEL REFINEMENT' ? Coot 8.9.6 ? 1 ? 15 'MODEL REFINEMENT' ? PHENIX 1.19.2-4158 ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 3 _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 'National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)' _pdbx_audit_support.country 'United States' _pdbx_audit_support.grant_number R35GM133325 _pdbx_audit_support.ordinal 1 # _atom_sites.entry_id 8DNA _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_