data_5LY6 # _entry.id 5LY6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.315 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 5LY6 WWPDB D_1200001559 EMDB EMD-4118 # _pdbx_database_related.db_name EMDB _pdbx_database_related.details 'CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A' _pdbx_database_related.db_id EMD-4118 _pdbx_database_related.content_type 'associated EM volume' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.entry_id 5LY6 _pdbx_database_status.recvd_initial_deposition_date 2016-09-24 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'van Pee, K.' 1 'Neuhaus, A.' 2 ;D'Imprima, E. ; 3 'Mills, D.J.' 4 'Kuehlbrandt, W.' 5 'Yildiz, O.' 6 # _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 Elife _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 2050-084X _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 6 _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.' _citation.year 2017 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.7554/eLife.23644 _citation.pdbx_database_id_PubMed 28323617 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'van Pee, K.' 1 ? primary 'Neuhaus, A.' 2 ? primary ;D'Imprima, E. ; 3 ? primary 'Mills, D.J.' 4 ? primary 'Kuhlbrandt, W.' 5 ? primary 'Yildiz, O.' 6 ? # _cell.angle_alpha 90.0 _cell.angle_alpha_esd ? _cell.angle_beta 90.0 _cell.angle_beta_esd ? _cell.angle_gamma 90.0 _cell.angle_gamma_esd ? _cell.entry_id 5LY6 _cell.details ? _cell.formula_units_Z ? _cell.length_a 1.0 _cell.length_a_esd ? _cell.length_b 1.0 _cell.length_b_esd ? _cell.length_c 1.0 _cell.length_c_esd ? _cell.volume ? _cell.volume_esd ? _cell.Z_PDB 1 _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 ? # _symmetry.entry_id 5LY6 _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 ? # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description Pneumolysin _entity.formula_weight 52866.066 _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 'Thiol-activated cytolysin' # _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 ;MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ LKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND ; _entity_poly.pdbx_seq_one_letter_code_can ;MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ LKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND ; _entity_poly.pdbx_strand_id B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ALA n 1 3 ASN n 1 4 LYS n 1 5 ALA n 1 6 VAL n 1 7 ASN n 1 8 ASP n 1 9 PHE n 1 10 ILE n 1 11 LEU n 1 12 ALA n 1 13 MET n 1 14 ASN n 1 15 TYR n 1 16 ASP n 1 17 LYS n 1 18 LYS n 1 19 LYS n 1 20 LEU n 1 21 LEU n 1 22 THR n 1 23 HIS n 1 24 GLN n 1 25 GLY n 1 26 GLU n 1 27 SER n 1 28 ILE n 1 29 GLU n 1 30 ASN n 1 31 ARG n 1 32 PHE n 1 33 ILE n 1 34 LYS n 1 35 GLU n 1 36 GLY n 1 37 ASN n 1 38 GLN n 1 39 LEU n 1 40 PRO n 1 41 ASP n 1 42 GLU n 1 43 PHE n 1 44 VAL n 1 45 VAL n 1 46 ILE n 1 47 GLU n 1 48 ARG n 1 49 LYS n 1 50 LYS n 1 51 ARG n 1 52 SER n 1 53 LEU n 1 54 SER n 1 55 THR n 1 56 ASN n 1 57 THR n 1 58 SER n 1 59 ASP n 1 60 ILE n 1 61 SER n 1 62 VAL n 1 63 THR n 1 64 ALA n 1 65 THR n 1 66 ASN n 1 67 ASP n 1 68 SER n 1 69 ARG n 1 70 LEU n 1 71 TYR n 1 72 PRO n 1 73 GLY n 1 74 ALA n 1 75 LEU n 1 76 LEU n 1 77 VAL n 1 78 VAL n 1 79 ASP n 1 80 GLU n 1 81 THR n 1 82 LEU n 1 83 LEU n 1 84 GLU n 1 85 ASN n 1 86 ASN n 1 87 PRO n 1 88 THR n 1 89 LEU n 1 90 LEU n 1 91 ALA n 1 92 VAL n 1 93 ASP n 1 94 ARG n 1 95 ALA n 1 96 PRO n 1 97 MET n 1 98 THR n 1 99 TYR n 1 100 SER n 1 101 ILE n 1 102 ASP n 1 103 LEU n 1 104 PRO n 1 105 GLY n 1 106 LEU n 1 107 ALA n 1 108 SER n 1 109 SER n 1 110 ASP n 1 111 SER n 1 112 PHE n 1 113 LEU n 1 114 GLN n 1 115 VAL n 1 116 GLU n 1 117 ASP n 1 118 PRO n 1 119 SER n 1 120 ASN n 1 121 SER n 1 122 SER n 1 123 VAL n 1 124 ARG n 1 125 GLY n 1 126 ALA n 1 127 VAL n 1 128 ASN n 1 129 ASP n 1 130 LEU n 1 131 LEU n 1 132 ALA n 1 133 LYS n 1 134 TRP n 1 135 HIS n 1 136 GLN n 1 137 ASP n 1 138 TYR n 1 139 GLY n 1 140 GLN n 1 141 VAL n 1 142 ASN n 1 143 ASN n 1 144 VAL n 1 145 PRO n 1 146 ALA n 1 147 ARG n 1 148 MET n 1 149 GLN n 1 150 TYR n 1 151 GLU n 1 152 LYS n 1 153 ILE n 1 154 THR n 1 155 ALA n 1 156 HIS n 1 157 SER n 1 158 MET n 1 159 GLU n 1 160 GLN n 1 161 LEU n 1 162 LYS n 1 163 VAL n 1 164 LYS n 1 165 PHE n 1 166 GLY n 1 167 SER n 1 168 ASP n 1 169 PHE n 1 170 GLU n 1 171 LYS n 1 172 ALA n 1 173 ALA n 1 174 ASN n 1 175 SER n 1 176 LEU n 1 177 ASP n 1 178 ILE n 1 179 ASP n 1 180 PHE n 1 181 ASN n 1 182 ALA n 1 183 VAL n 1 184 HIS n 1 185 SER n 1 186 GLY n 1 187 GLU n 1 188 LYS n 1 189 GLN n 1 190 ILE n 1 191 GLN n 1 192 ILE n 1 193 VAL n 1 194 ASN n 1 195 PHE n 1 196 LYS n 1 197 GLN n 1 198 ILE n 1 199 TYR n 1 200 TYR n 1 201 THR n 1 202 VAL n 1 203 SER n 1 204 VAL n 1 205 ASP n 1 206 ALA n 1 207 VAL n 1 208 LYS n 1 209 ASN n 1 210 PRO n 1 211 GLY n 1 212 ASP n 1 213 VAL n 1 214 PHE n 1 215 GLN n 1 216 ASP n 1 217 THR n 1 218 VAL n 1 219 THR n 1 220 VAL n 1 221 GLU n 1 222 ASP n 1 223 LEU n 1 224 LYS n 1 225 GLN n 1 226 ARG n 1 227 GLY n 1 228 ILE n 1 229 SER n 1 230 ALA n 1 231 GLU n 1 232 ARG n 1 233 PRO n 1 234 LEU n 1 235 VAL n 1 236 TYR n 1 237 ILE n 1 238 SER n 1 239 SER n 1 240 VAL n 1 241 ALA n 1 242 TYR n 1 243 GLY n 1 244 ARG n 1 245 GLN n 1 246 VAL n 1 247 TYR n 1 248 LEU n 1 249 LYS n 1 250 LEU n 1 251 GLU n 1 252 THR n 1 253 THR n 1 254 SER n 1 255 LYS n 1 256 SER n 1 257 ASP n 1 258 GLU n 1 259 VAL n 1 260 GLN n 1 261 ALA n 1 262 ALA n 1 263 PHE n 1 264 GLU n 1 265 ALA n 1 266 ALA n 1 267 ILE n 1 268 LEU n 1 269 GLY n 1 270 VAL n 1 271 LYS n 1 272 VAL n 1 273 ALA n 1 274 PRO n 1 275 GLN n 1 276 THR n 1 277 GLN n 1 278 TRP n 1 279 LYS n 1 280 GLN n 1 281 ILE n 1 282 LEU n 1 283 ASP n 1 284 ASN n 1 285 THR n 1 286 GLU n 1 287 VAL n 1 288 LYS n 1 289 ALA n 1 290 VAL n 1 291 ILE n 1 292 LEU n 1 293 GLY n 1 294 GLY n 1 295 ASP n 1 296 PRO n 1 297 SER n 1 298 SER n 1 299 GLY n 1 300 ALA n 1 301 ARG n 1 302 VAL n 1 303 VAL n 1 304 THR n 1 305 GLY n 1 306 LYS n 1 307 VAL n 1 308 ASP n 1 309 MET n 1 310 VAL n 1 311 GLU n 1 312 ASP n 1 313 LEU n 1 314 ILE n 1 315 GLN n 1 316 GLU n 1 317 GLY n 1 318 SER n 1 319 ARG n 1 320 PHE n 1 321 THR n 1 322 ALA n 1 323 ASP n 1 324 HIS n 1 325 PRO n 1 326 GLY n 1 327 LEU n 1 328 PRO n 1 329 ILE n 1 330 SER n 1 331 TYR n 1 332 THR n 1 333 THR n 1 334 SER n 1 335 PHE n 1 336 LEU n 1 337 ARG n 1 338 ASP n 1 339 ASN n 1 340 VAL n 1 341 VAL n 1 342 ALA n 1 343 THR n 1 344 PHE n 1 345 GLN n 1 346 ASN n 1 347 SER n 1 348 THR n 1 349 ASP n 1 350 TYR n 1 351 VAL n 1 352 GLU n 1 353 THR n 1 354 LYS n 1 355 VAL n 1 356 THR n 1 357 ALA n 1 358 TYR n 1 359 ARG n 1 360 ASN n 1 361 GLY n 1 362 ASP n 1 363 LEU n 1 364 LEU n 1 365 LEU n 1 366 ASP n 1 367 HIS n 1 368 SER n 1 369 GLY n 1 370 ALA n 1 371 TYR n 1 372 VAL n 1 373 ALA n 1 374 GLN n 1 375 TYR n 1 376 TYR n 1 377 ILE n 1 378 THR n 1 379 TRP n 1 380 ASP n 1 381 GLU n 1 382 LEU n 1 383 SER n 1 384 TYR n 1 385 ASP n 1 386 HIS n 1 387 GLN n 1 388 GLY n 1 389 LYS n 1 390 GLU n 1 391 VAL n 1 392 LEU n 1 393 THR n 1 394 PRO n 1 395 LYS n 1 396 ALA n 1 397 TRP n 1 398 ASP n 1 399 ARG n 1 400 ASN n 1 401 GLY n 1 402 GLN n 1 403 ASP n 1 404 LEU n 1 405 THR n 1 406 ALA n 1 407 HIS n 1 408 PHE n 1 409 THR n 1 410 THR n 1 411 SER n 1 412 ILE n 1 413 PRO n 1 414 LEU n 1 415 LYS n 1 416 GLY n 1 417 ASN n 1 418 VAL n 1 419 ARG n 1 420 ASN n 1 421 LEU n 1 422 SER n 1 423 VAL n 1 424 LYS n 1 425 ILE n 1 426 ARG n 1 427 GLU n 1 428 CYS n 1 429 THR n 1 430 GLY n 1 431 LEU n 1 432 ALA n 1 433 TRP n 1 434 GLU n 1 435 TRP n 1 436 TRP n 1 437 ARG n 1 438 THR n 1 439 VAL n 1 440 TYR n 1 441 GLU n 1 442 LYS n 1 443 THR n 1 444 ASP n 1 445 LEU n 1 446 PRO n 1 447 LEU n 1 448 VAL n 1 449 ARG n 1 450 LYS n 1 451 ARG n 1 452 THR n 1 453 ILE n 1 454 SER n 1 455 ILE n 1 456 TRP n 1 457 GLY n 1 458 THR n 1 459 THR n 1 460 LEU n 1 461 TYR n 1 462 PRO n 1 463 GLN n 1 464 VAL n 1 465 GLU n 1 466 ASP n 1 467 LYS n 1 468 VAL n 1 469 GLU n 1 470 ASN n 1 471 ASP 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 471 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'ply, SPD_1726' _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 'Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 373153 _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 ? _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 TACY_STRP2 _struct_ref.pdbx_db_accession Q04IN8 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ LKVKFGSDFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV AYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND ; _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 5LY6 _struct_ref_seq.pdbx_strand_id B _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 471 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q04IN8 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 471 _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 471 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 5LY6 ALA B 172 ? UNP Q04IN8 THR 172 conflict 172 1 1 5LY6 ALA B 173 ? UNP Q04IN8 GLY 173 conflict 173 2 1 5LY6 ALA B 182 ? UNP Q04IN8 SER 182 conflict 182 3 1 5LY6 GLN B 260 ? UNP Q04IN8 GLU 260 conflict 260 4 1 5LY6 ALA B 266 ? UNP Q04IN8 LEU 266 conflict 266 5 1 5LY6 LEU B 268 ? UNP Q04IN8 LYS 268 conflict 268 6 1 5LY6 GLN B 277 ? UNP Q04IN8 GLU 277 conflict 277 7 # 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 # _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 5LY6 _exptl.crystals_number ? _exptl.details ? _exptl.method 'ELECTRON MICROSCOPY' _exptl.method_details ? # _struct.entry_id 5LY6 _struct.title 'CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A' _struct.pdbx_descriptor Pneumolysin _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 5LY6 _struct_keywords.text 'Bacterial toxins, pore complex, cryoEM structure, cholesterol-dependent cytolysin, Pneumolysin, membrane pore, TOXIN' _struct_keywords.pdbx_keywords TOXIN # _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 ? # 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 1 ALA A 2 ? ALA A 12 ? ALA B 2 ALA B 12 1 ? 11 HELX_P HELX_P2 2 LYS A 17 ? LEU A 21 ? LYS B 17 LEU B 21 1 ? 5 HELX_P HELX_P3 3 ASP A 59 ? ASP A 67 ? ASP B 59 ASP B 67 1 ? 9 HELX_P HELX_P4 4 SER A 122 ? ASP A 137 ? SER B 122 ASP B 137 1 ? 16 HELX_P HELX_P5 5 ASP A 222 ? GLY A 227 ? ASP B 222 GLY B 227 1 ? 6 HELX_P HELX_P6 6 SER A 297 ? THR A 304 ? SER B 297 THR B 304 1 ? 8 HELX_P HELX_P7 7 VAL A 310 ? LEU A 313 ? VAL B 310 LEU B 313 1 ? 4 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id ALA _struct_mon_prot_cis.label_seq_id 406 _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 406 _struct_mon_prot_cis.auth_asym_id B _struct_mon_prot_cis.pdbx_label_comp_id_2 HIS _struct_mon_prot_cis.pdbx_label_seq_id_2 407 _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 HIS _struct_mon_prot_cis.pdbx_auth_seq_id_2 407 _struct_mon_prot_cis.pdbx_auth_asym_id_2 B _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle 0.00 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 3 ? B ? 2 ? C ? 4 ? D ? 2 ? E ? 3 ? F ? 2 ? G ? 4 ? H ? 2 ? I ? 2 ? J ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel B 1 2 ? anti-parallel C 1 2 ? anti-parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel D 1 2 ? anti-parallel E 1 2 ? anti-parallel E 2 3 ? anti-parallel F 1 2 ? anti-parallel G 1 2 ? anti-parallel G 2 3 ? parallel G 3 4 ? anti-parallel H 1 2 ? anti-parallel I 1 2 ? anti-parallel J 1 2 ? anti-parallel J 2 3 ? 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 A 1 ILE A 28 ? ARG A 31 ? ILE B 28 ARG B 31 A 2 PHE A 43 ? ARG A 48 ? PHE B 43 ARG B 48 A 3 GLU A 352 ? ALA A 357 ? GLU B 352 ALA B 357 B 1 TYR A 99 ? ILE A 101 ? TYR B 99 ILE B 101 B 2 VAL A 202 ? VAL A 204 ? VAL B 202 VAL B 204 C 1 ARG A 147 ? GLN A 149 ? ARG B 147 GLN B 149 C 2 PHE A 180 ? ILE A 198 ? PHE B 180 ILE B 198 C 3 GLY A 243 ? ALA A 261 ? GLY B 243 ALA B 261 C 4 ILE A 281 ? LYS A 288 ? ILE B 281 LYS B 288 D 1 LYS A 152 ? PHE A 165 ? LYS B 152 PHE B 165 D 2 PHE A 180 ? VAL A 193 ? PHE B 180 VAL B 193 E 1 VAL A 235 ? ILE A 237 ? VAL B 235 ILE B 237 E 2 TYR A 331 ? PHE A 335 ? TYR B 331 PHE B 335 E 3 ALA A 342 ? GLN A 345 ? ALA B 342 GLN B 345 F 1 ALA A 261 ? GLU A 264 ? ALA B 261 GLU B 264 F 2 ALA A 273 ? THR A 276 ? ALA B 273 THR B 276 G 1 PHE A 408 ? PRO A 413 ? PHE B 408 PRO B 413 G 2 ASP A 362 ? GLY A 369 ? ASP B 362 GLY B 369 G 3 LYS A 450 ? GLY A 457 ? LYS B 450 GLY B 457 G 4 GLN A 463 ? GLU A 469 ? GLN B 463 GLU B 469 H 1 VAL A 372 ? GLN A 374 ? VAL B 372 GLN B 374 H 2 ARG A 426 ? CYS A 428 ? ARG B 426 CYS B 428 I 1 LEU A 382 ? TYR A 384 ? LEU B 382 TYR B 384 I 2 GLU A 390 ? LEU A 392 ? GLU B 390 LEU B 392 J 1 TYR A 440 ? LYS A 442 ? TYR B 440 LYS B 442 J 2 ARG A 419 ? ILE A 425 ? ARG B 419 ILE B 425 J 3 ILE A 377 ? ASP A 380 ? ILE B 377 ASP B 380 # 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 A 1 2 O GLU A 29 ? O GLU B 29 N ILE A 46 ? N ILE B 46 A 2 3 O PHE A 43 ? O PHE B 43 N ALA A 357 ? N ALA B 357 B 1 2 O SER A 100 ? O SER B 100 N SER A 203 ? N SER B 203 C 1 2 O ARG A 147 ? O ARG B 147 N ILE A 198 ? N ILE B 198 C 2 3 O ASN A 181 ? O ASN B 181 N GLN A 260 ? N GLN B 260 C 3 4 O LYS A 249 ? O LYS B 249 N LYS A 288 ? N LYS B 288 D 1 2 O ILE A 153 ? O ILE B 153 N ILE A 192 ? N ILE B 192 E 1 2 O TYR A 236 ? O TYR B 236 N SER A 334 ? N SER B 334 E 2 3 O TYR A 331 ? O TYR B 331 N GLN A 345 ? N GLN B 345 F 1 2 O ALA A 261 ? O ALA B 261 N THR A 276 ? N THR B 276 G 1 2 O PHE A 408 ? O PHE B 408 N HIS A 367 ? N HIS B 367 G 2 3 O ASP A 362 ? O ASP B 362 N ARG A 451 ? N ARG B 451 G 3 4 O LYS A 450 ? O LYS B 450 N GLU A 469 ? N GLU B 469 H 1 2 O VAL A 372 ? O VAL B 372 N CYS A 428 ? N CYS B 428 I 1 2 O SER A 383 ? O SER B 383 N VAL A 391 ? N VAL B 391 J 1 2 O TYR A 440 ? O TYR B 440 N ILE A 425 ? N ILE B 425 J 2 3 O ARG A 419 ? O ARG B 419 N ASP A 380 ? N ASP B 380 # _atom_sites.entry_id 5LY6 _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 # loop_ _atom_type.symbol C N O S # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 MET 1 1 1 MET MET B . n A 1 2 ALA 2 2 2 ALA ALA B . n A 1 3 ASN 3 3 3 ASN ASN B . n A 1 4 LYS 4 4 4 LYS LYS B . n A 1 5 ALA 5 5 5 ALA ALA B . n A 1 6 VAL 6 6 6 VAL VAL B . n A 1 7 ASN 7 7 7 ASN ASN B . n A 1 8 ASP 8 8 8 ASP ASP B . n A 1 9 PHE 9 9 9 PHE PHE B . n A 1 10 ILE 10 10 10 ILE ILE B . n A 1 11 LEU 11 11 11 LEU LEU B . n A 1 12 ALA 12 12 12 ALA ALA B . n A 1 13 MET 13 13 13 MET MET B . n A 1 14 ASN 14 14 14 ASN ASN B . n A 1 15 TYR 15 15 15 TYR TYR B . n A 1 16 ASP 16 16 16 ASP ASP B . n A 1 17 LYS 17 17 17 LYS LYS B . n A 1 18 LYS 18 18 18 LYS LYS B . n A 1 19 LYS 19 19 19 LYS LYS B . n A 1 20 LEU 20 20 20 LEU LEU B . n A 1 21 LEU 21 21 21 LEU LEU B . n A 1 22 THR 22 22 22 THR THR B . n A 1 23 HIS 23 23 23 HIS HIS B . n A 1 24 GLN 24 24 24 GLN GLN B . n A 1 25 GLY 25 25 25 GLY GLY B . n A 1 26 GLU 26 26 26 GLU GLU B . n A 1 27 SER 27 27 27 SER SER B . n A 1 28 ILE 28 28 28 ILE ILE B . n A 1 29 GLU 29 29 29 GLU GLU B . n A 1 30 ASN 30 30 30 ASN ASN B . n A 1 31 ARG 31 31 31 ARG ARG B . n A 1 32 PHE 32 32 32 PHE PHE B . n A 1 33 ILE 33 33 33 ILE ILE B . n A 1 34 LYS 34 34 34 LYS LYS B . n A 1 35 GLU 35 35 35 GLU GLU B . n A 1 36 GLY 36 36 36 GLY GLY B . n A 1 37 ASN 37 37 37 ASN ASN B . n A 1 38 GLN 38 38 38 GLN GLN B . n A 1 39 LEU 39 39 39 LEU LEU B . n A 1 40 PRO 40 40 40 PRO PRO B . n A 1 41 ASP 41 41 41 ASP ASP B . n A 1 42 GLU 42 42 42 GLU GLU B . n A 1 43 PHE 43 43 43 PHE PHE B . n A 1 44 VAL 44 44 44 VAL VAL B . n A 1 45 VAL 45 45 45 VAL VAL B . n A 1 46 ILE 46 46 46 ILE ILE B . n A 1 47 GLU 47 47 47 GLU GLU B . n A 1 48 ARG 48 48 48 ARG ARG B . n A 1 49 LYS 49 49 49 LYS LYS B . n A 1 50 LYS 50 50 50 LYS LYS B . n A 1 51 ARG 51 51 51 ARG ARG B . n A 1 52 SER 52 52 52 SER SER B . n A 1 53 LEU 53 53 53 LEU LEU B . n A 1 54 SER 54 54 54 SER SER B . n A 1 55 THR 55 55 55 THR THR B . n A 1 56 ASN 56 56 56 ASN ASN B . n A 1 57 THR 57 57 57 THR THR B . n A 1 58 SER 58 58 58 SER SER B . n A 1 59 ASP 59 59 59 ASP ASP B . n A 1 60 ILE 60 60 60 ILE ILE B . n A 1 61 SER 61 61 61 SER SER B . n A 1 62 VAL 62 62 62 VAL VAL B . n A 1 63 THR 63 63 63 THR THR B . n A 1 64 ALA 64 64 64 ALA ALA B . n A 1 65 THR 65 65 65 THR THR B . n A 1 66 ASN 66 66 66 ASN ASN B . n A 1 67 ASP 67 67 67 ASP ASP B . n A 1 68 SER 68 68 68 SER SER B . n A 1 69 ARG 69 69 69 ARG ARG B . n A 1 70 LEU 70 70 70 LEU LEU B . n A 1 71 TYR 71 71 71 TYR TYR B . n A 1 72 PRO 72 72 72 PRO PRO B . n A 1 73 GLY 73 73 73 GLY GLY B . n A 1 74 ALA 74 74 74 ALA ALA B . n A 1 75 LEU 75 75 75 LEU LEU B . n A 1 76 LEU 76 76 76 LEU LEU B . n A 1 77 VAL 77 77 77 VAL VAL B . n A 1 78 VAL 78 78 78 VAL VAL B . n A 1 79 ASP 79 79 79 ASP ASP B . n A 1 80 GLU 80 80 80 GLU GLU B . n A 1 81 THR 81 81 81 THR THR B . n A 1 82 LEU 82 82 82 LEU LEU B . n A 1 83 LEU 83 83 83 LEU LEU B . n A 1 84 GLU 84 84 84 GLU GLU B . n A 1 85 ASN 85 85 85 ASN ASN B . n A 1 86 ASN 86 86 86 ASN ASN B . n A 1 87 PRO 87 87 87 PRO PRO B . n A 1 88 THR 88 88 88 THR THR B . n A 1 89 LEU 89 89 89 LEU LEU B . n A 1 90 LEU 90 90 90 LEU LEU B . n A 1 91 ALA 91 91 91 ALA ALA B . n A 1 92 VAL 92 92 92 VAL VAL B . n A 1 93 ASP 93 93 93 ASP ASP B . n A 1 94 ARG 94 94 94 ARG ARG B . n A 1 95 ALA 95 95 95 ALA ALA B . n A 1 96 PRO 96 96 96 PRO PRO B . n A 1 97 MET 97 97 97 MET MET B . n A 1 98 THR 98 98 98 THR THR B . n A 1 99 TYR 99 99 99 TYR TYR B . n A 1 100 SER 100 100 100 SER SER B . n A 1 101 ILE 101 101 101 ILE ILE B . n A 1 102 ASP 102 102 102 ASP ASP B . n A 1 103 LEU 103 103 103 LEU LEU B . n A 1 104 PRO 104 104 104 PRO PRO B . n A 1 105 GLY 105 105 105 GLY GLY B . n A 1 106 LEU 106 106 106 LEU LEU B . n A 1 107 ALA 107 107 107 ALA ALA B . n A 1 108 SER 108 108 108 SER SER B . n A 1 109 SER 109 109 109 SER SER B . n A 1 110 ASP 110 110 110 ASP ASP B . n A 1 111 SER 111 111 111 SER SER B . n A 1 112 PHE 112 112 112 PHE PHE B . n A 1 113 LEU 113 113 113 LEU LEU B . n A 1 114 GLN 114 114 114 GLN GLN B . n A 1 115 VAL 115 115 115 VAL VAL B . n A 1 116 GLU 116 116 116 GLU GLU B . n A 1 117 ASP 117 117 117 ASP ASP B . n A 1 118 PRO 118 118 118 PRO PRO B . n A 1 119 SER 119 119 119 SER SER B . n A 1 120 ASN 120 120 120 ASN ASN B . n A 1 121 SER 121 121 121 SER SER B . n A 1 122 SER 122 122 122 SER SER B . n A 1 123 VAL 123 123 123 VAL VAL B . n A 1 124 ARG 124 124 124 ARG ARG B . n A 1 125 GLY 125 125 125 GLY GLY B . n A 1 126 ALA 126 126 126 ALA ALA B . n A 1 127 VAL 127 127 127 VAL VAL B . n A 1 128 ASN 128 128 128 ASN ASN B . n A 1 129 ASP 129 129 129 ASP ASP B . n A 1 130 LEU 130 130 130 LEU LEU B . n A 1 131 LEU 131 131 131 LEU LEU B . n A 1 132 ALA 132 132 132 ALA ALA B . n A 1 133 LYS 133 133 133 LYS LYS B . n A 1 134 TRP 134 134 134 TRP TRP B . n A 1 135 HIS 135 135 135 HIS HIS B . n A 1 136 GLN 136 136 136 GLN GLN B . n A 1 137 ASP 137 137 137 ASP ASP B . n A 1 138 TYR 138 138 138 TYR TYR B . n A 1 139 GLY 139 139 139 GLY GLY B . n A 1 140 GLN 140 140 140 GLN GLN B . n A 1 141 VAL 141 141 141 VAL VAL B . n A 1 142 ASN 142 142 142 ASN ASN B . n A 1 143 ASN 143 143 143 ASN ASN B . n A 1 144 VAL 144 144 144 VAL VAL B . n A 1 145 PRO 145 145 145 PRO PRO B . n A 1 146 ALA 146 146 146 ALA ALA B . n A 1 147 ARG 147 147 147 ARG ARG B . n A 1 148 MET 148 148 148 MET MET B . n A 1 149 GLN 149 149 149 GLN GLN B . n A 1 150 TYR 150 150 150 TYR TYR B . n A 1 151 GLU 151 151 151 GLU GLU B . n A 1 152 LYS 152 152 152 LYS LYS B . n A 1 153 ILE 153 153 153 ILE ILE B . n A 1 154 THR 154 154 154 THR THR B . n A 1 155 ALA 155 155 155 ALA ALA B . n A 1 156 HIS 156 156 156 HIS HIS B . n A 1 157 SER 157 157 157 SER SER B . n A 1 158 MET 158 158 158 MET MET B . n A 1 159 GLU 159 159 159 GLU GLU B . n A 1 160 GLN 160 160 160 GLN GLN B . n A 1 161 LEU 161 161 161 LEU LEU B . n A 1 162 LYS 162 162 162 LYS LYS B . n A 1 163 VAL 163 163 163 VAL VAL B . n A 1 164 LYS 164 164 164 LYS LYS B . n A 1 165 PHE 165 165 165 PHE PHE B . n A 1 166 GLY 166 166 166 GLY GLY B . n A 1 167 SER 167 167 167 SER SER B . n A 1 168 ASP 168 168 168 ASP ASP B . n A 1 169 PHE 169 169 169 PHE PHE B . n A 1 170 GLU 170 170 170 GLU GLU B . n A 1 171 LYS 171 171 171 LYS LYS B . n A 1 172 ALA 172 172 172 ALA ALA B . n A 1 173 ALA 173 173 173 ALA ALA B . n A 1 174 ASN 174 174 174 ASN ASN B . n A 1 175 SER 175 175 175 SER SER B . n A 1 176 LEU 176 176 176 LEU LEU B . n A 1 177 ASP 177 177 177 ASP ASP B . n A 1 178 ILE 178 178 178 ILE ILE B . n A 1 179 ASP 179 179 179 ASP ASP B . n A 1 180 PHE 180 180 180 PHE PHE B . n A 1 181 ASN 181 181 181 ASN ASN B . n A 1 182 ALA 182 182 182 ALA ALA B . n A 1 183 VAL 183 183 183 VAL VAL B . n A 1 184 HIS 184 184 184 HIS HIS B . n A 1 185 SER 185 185 185 SER SER B . n A 1 186 GLY 186 186 186 GLY GLY B . n A 1 187 GLU 187 187 187 GLU GLU B . n A 1 188 LYS 188 188 188 LYS LYS B . n A 1 189 GLN 189 189 189 GLN GLN B . n A 1 190 ILE 190 190 190 ILE ILE B . n A 1 191 GLN 191 191 191 GLN GLN B . n A 1 192 ILE 192 192 192 ILE ILE B . n A 1 193 VAL 193 193 193 VAL VAL B . n A 1 194 ASN 194 194 194 ASN ASN B . n A 1 195 PHE 195 195 195 PHE PHE B . n A 1 196 LYS 196 196 196 LYS LYS B . n A 1 197 GLN 197 197 197 GLN GLN B . n A 1 198 ILE 198 198 198 ILE ILE B . n A 1 199 TYR 199 199 199 TYR TYR B . n A 1 200 TYR 200 200 200 TYR TYR B . n A 1 201 THR 201 201 201 THR THR B . n A 1 202 VAL 202 202 202 VAL VAL B . n A 1 203 SER 203 203 203 SER SER B . n A 1 204 VAL 204 204 204 VAL VAL B . n A 1 205 ASP 205 205 205 ASP ASP B . n A 1 206 ALA 206 206 206 ALA ALA B . n A 1 207 VAL 207 207 207 VAL VAL B . n A 1 208 LYS 208 208 208 LYS LYS B . n A 1 209 ASN 209 209 209 ASN ASN B . n A 1 210 PRO 210 210 210 PRO PRO B . n A 1 211 GLY 211 211 211 GLY GLY B . n A 1 212 ASP 212 212 212 ASP ASP B . n A 1 213 VAL 213 213 213 VAL VAL B . n A 1 214 PHE 214 214 214 PHE PHE B . n A 1 215 GLN 215 215 215 GLN GLN B . n A 1 216 ASP 216 216 216 ASP ASP B . n A 1 217 THR 217 217 217 THR THR B . n A 1 218 VAL 218 218 218 VAL VAL B . n A 1 219 THR 219 219 219 THR THR B . n A 1 220 VAL 220 220 220 VAL VAL B . n A 1 221 GLU 221 221 221 GLU GLU B . n A 1 222 ASP 222 222 222 ASP ASP B . n A 1 223 LEU 223 223 223 LEU LEU B . n A 1 224 LYS 224 224 224 LYS LYS B . n A 1 225 GLN 225 225 225 GLN GLN B . n A 1 226 ARG 226 226 226 ARG ARG B . n A 1 227 GLY 227 227 227 GLY GLY B . n A 1 228 ILE 228 228 228 ILE ILE B . n A 1 229 SER 229 229 229 SER SER B . n A 1 230 ALA 230 230 230 ALA ALA B . n A 1 231 GLU 231 231 231 GLU GLU B . n A 1 232 ARG 232 232 232 ARG ARG B . n A 1 233 PRO 233 233 233 PRO PRO B . n A 1 234 LEU 234 234 234 LEU LEU B . n A 1 235 VAL 235 235 235 VAL VAL B . n A 1 236 TYR 236 236 236 TYR TYR B . n A 1 237 ILE 237 237 237 ILE ILE B . n A 1 238 SER 238 238 238 SER SER B . n A 1 239 SER 239 239 239 SER SER B . n A 1 240 VAL 240 240 240 VAL VAL B . n A 1 241 ALA 241 241 241 ALA ALA B . n A 1 242 TYR 242 242 242 TYR TYR B . n A 1 243 GLY 243 243 243 GLY GLY B . n A 1 244 ARG 244 244 244 ARG ARG B . n A 1 245 GLN 245 245 245 GLN GLN B . n A 1 246 VAL 246 246 246 VAL VAL B . n A 1 247 TYR 247 247 247 TYR TYR B . n A 1 248 LEU 248 248 248 LEU LEU B . n A 1 249 LYS 249 249 249 LYS LYS B . n A 1 250 LEU 250 250 250 LEU LEU B . n A 1 251 GLU 251 251 251 GLU GLU B . n A 1 252 THR 252 252 252 THR THR B . n A 1 253 THR 253 253 253 THR THR B . n A 1 254 SER 254 254 254 SER SER B . n A 1 255 LYS 255 255 255 LYS LYS B . n A 1 256 SER 256 256 256 SER SER B . n A 1 257 ASP 257 257 257 ASP ASP B . n A 1 258 GLU 258 258 258 GLU GLU B . n A 1 259 VAL 259 259 259 VAL VAL B . n A 1 260 GLN 260 260 260 GLN GLN B . n A 1 261 ALA 261 261 261 ALA ALA B . n A 1 262 ALA 262 262 262 ALA ALA B . n A 1 263 PHE 263 263 263 PHE PHE B . n A 1 264 GLU 264 264 264 GLU GLU B . n A 1 265 ALA 265 265 265 ALA ALA B . n A 1 266 ALA 266 266 266 ALA ALA B . n A 1 267 ILE 267 267 267 ILE ILE B . n A 1 268 LEU 268 268 268 LEU LEU B . n A 1 269 GLY 269 269 269 GLY GLY B . n A 1 270 VAL 270 270 270 VAL VAL B . n A 1 271 LYS 271 271 271 LYS LYS B . n A 1 272 VAL 272 272 272 VAL VAL B . n A 1 273 ALA 273 273 273 ALA ALA B . n A 1 274 PRO 274 274 274 PRO PRO B . n A 1 275 GLN 275 275 275 GLN GLN B . n A 1 276 THR 276 276 276 THR THR B . n A 1 277 GLN 277 277 277 GLN GLN B . n A 1 278 TRP 278 278 278 TRP TRP B . n A 1 279 LYS 279 279 279 LYS LYS B . n A 1 280 GLN 280 280 280 GLN GLN B . n A 1 281 ILE 281 281 281 ILE ILE B . n A 1 282 LEU 282 282 282 LEU LEU B . n A 1 283 ASP 283 283 283 ASP ASP B . n A 1 284 ASN 284 284 284 ASN ASN B . n A 1 285 THR 285 285 285 THR THR B . n A 1 286 GLU 286 286 286 GLU GLU B . n A 1 287 VAL 287 287 287 VAL VAL B . n A 1 288 LYS 288 288 288 LYS LYS B . n A 1 289 ALA 289 289 289 ALA ALA B . n A 1 290 VAL 290 290 290 VAL VAL B . n A 1 291 ILE 291 291 291 ILE ILE B . n A 1 292 LEU 292 292 292 LEU LEU B . n A 1 293 GLY 293 293 293 GLY GLY B . n A 1 294 GLY 294 294 294 GLY GLY B . n A 1 295 ASP 295 295 295 ASP ASP B . n A 1 296 PRO 296 296 296 PRO PRO B . n A 1 297 SER 297 297 297 SER SER B . n A 1 298 SER 298 298 298 SER SER B . n A 1 299 GLY 299 299 299 GLY GLY B . n A 1 300 ALA 300 300 300 ALA ALA B . n A 1 301 ARG 301 301 301 ARG ARG B . n A 1 302 VAL 302 302 302 VAL VAL B . n A 1 303 VAL 303 303 303 VAL VAL B . n A 1 304 THR 304 304 304 THR THR B . n A 1 305 GLY 305 305 305 GLY GLY B . n A 1 306 LYS 306 306 306 LYS LYS B . n A 1 307 VAL 307 307 307 VAL VAL B . n A 1 308 ASP 308 308 308 ASP ASP B . n A 1 309 MET 309 309 309 MET MET B . n A 1 310 VAL 310 310 310 VAL VAL B . n A 1 311 GLU 311 311 311 GLU GLU B . n A 1 312 ASP 312 312 312 ASP ASP B . n A 1 313 LEU 313 313 313 LEU LEU B . n A 1 314 ILE 314 314 314 ILE ILE B . n A 1 315 GLN 315 315 315 GLN GLN B . n A 1 316 GLU 316 316 316 GLU GLU B . n A 1 317 GLY 317 317 317 GLY GLY B . n A 1 318 SER 318 318 318 SER SER B . n A 1 319 ARG 319 319 319 ARG ARG B . n A 1 320 PHE 320 320 320 PHE PHE B . n A 1 321 THR 321 321 321 THR THR B . n A 1 322 ALA 322 322 322 ALA ALA B . n A 1 323 ASP 323 323 323 ASP ASP B . n A 1 324 HIS 324 324 324 HIS HIS B . n A 1 325 PRO 325 325 325 PRO PRO B . n A 1 326 GLY 326 326 326 GLY GLY B . n A 1 327 LEU 327 327 327 LEU LEU B . n A 1 328 PRO 328 328 328 PRO PRO B . n A 1 329 ILE 329 329 329 ILE ILE B . n A 1 330 SER 330 330 330 SER SER B . n A 1 331 TYR 331 331 331 TYR TYR B . n A 1 332 THR 332 332 332 THR THR B . n A 1 333 THR 333 333 333 THR THR B . n A 1 334 SER 334 334 334 SER SER B . n A 1 335 PHE 335 335 335 PHE PHE B . n A 1 336 LEU 336 336 336 LEU LEU B . n A 1 337 ARG 337 337 337 ARG ARG B . n A 1 338 ASP 338 338 338 ASP ASP B . n A 1 339 ASN 339 339 339 ASN ASN B . n A 1 340 VAL 340 340 340 VAL VAL B . n A 1 341 VAL 341 341 341 VAL VAL B . n A 1 342 ALA 342 342 342 ALA ALA B . n A 1 343 THR 343 343 343 THR THR B . n A 1 344 PHE 344 344 344 PHE PHE B . n A 1 345 GLN 345 345 345 GLN GLN B . n A 1 346 ASN 346 346 346 ASN ASN B . n A 1 347 SER 347 347 347 SER SER B . n A 1 348 THR 348 348 348 THR THR B . n A 1 349 ASP 349 349 349 ASP ASP B . n A 1 350 TYR 350 350 350 TYR TYR B . n A 1 351 VAL 351 351 351 VAL VAL B . n A 1 352 GLU 352 352 352 GLU GLU B . n A 1 353 THR 353 353 353 THR THR B . n A 1 354 LYS 354 354 354 LYS LYS B . n A 1 355 VAL 355 355 355 VAL VAL B . n A 1 356 THR 356 356 356 THR THR B . n A 1 357 ALA 357 357 357 ALA ALA B . n A 1 358 TYR 358 358 358 TYR TYR B . n A 1 359 ARG 359 359 359 ARG ARG B . n A 1 360 ASN 360 360 360 ASN ASN B . n A 1 361 GLY 361 361 361 GLY GLY B . n A 1 362 ASP 362 362 362 ASP ASP B . n A 1 363 LEU 363 363 363 LEU LEU B . n A 1 364 LEU 364 364 364 LEU LEU B . n A 1 365 LEU 365 365 365 LEU LEU B . n A 1 366 ASP 366 366 366 ASP ASP B . n A 1 367 HIS 367 367 367 HIS HIS B . n A 1 368 SER 368 368 368 SER SER B . n A 1 369 GLY 369 369 369 GLY GLY B . n A 1 370 ALA 370 370 370 ALA ALA B . n A 1 371 TYR 371 371 371 TYR TYR B . n A 1 372 VAL 372 372 372 VAL VAL B . n A 1 373 ALA 373 373 373 ALA ALA B . n A 1 374 GLN 374 374 374 GLN GLN B . n A 1 375 TYR 375 375 375 TYR TYR B . n A 1 376 TYR 376 376 376 TYR TYR B . n A 1 377 ILE 377 377 377 ILE ILE B . n A 1 378 THR 378 378 378 THR THR B . n A 1 379 TRP 379 379 379 TRP TRP B . n A 1 380 ASP 380 380 380 ASP ASP B . n A 1 381 GLU 381 381 381 GLU GLU B . n A 1 382 LEU 382 382 382 LEU LEU B . n A 1 383 SER 383 383 383 SER SER B . n A 1 384 TYR 384 384 384 TYR TYR B . n A 1 385 ASP 385 385 385 ASP ASP B . n A 1 386 HIS 386 386 386 HIS HIS B . n A 1 387 GLN 387 387 387 GLN GLN B . n A 1 388 GLY 388 388 388 GLY GLY B . n A 1 389 LYS 389 389 389 LYS LYS B . n A 1 390 GLU 390 390 390 GLU GLU B . n A 1 391 VAL 391 391 391 VAL VAL B . n A 1 392 LEU 392 392 392 LEU LEU B . n A 1 393 THR 393 393 393 THR THR B . n A 1 394 PRO 394 394 394 PRO PRO B . n A 1 395 LYS 395 395 395 LYS LYS B . n A 1 396 ALA 396 396 396 ALA ALA B . n A 1 397 TRP 397 397 397 TRP TRP B . n A 1 398 ASP 398 398 398 ASP ASP B . n A 1 399 ARG 399 399 399 ARG ARG B . n A 1 400 ASN 400 400 400 ASN ASN B . n A 1 401 GLY 401 401 401 GLY GLY B . n A 1 402 GLN 402 402 402 GLN GLN B . n A 1 403 ASP 403 403 403 ASP ASP B . n A 1 404 LEU 404 404 404 LEU LEU B . n A 1 405 THR 405 405 405 THR THR B . n A 1 406 ALA 406 406 406 ALA ALA B . n A 1 407 HIS 407 407 407 HIS HIS B . n A 1 408 PHE 408 408 408 PHE PHE B . n A 1 409 THR 409 409 409 THR THR B . n A 1 410 THR 410 410 410 THR THR B . n A 1 411 SER 411 411 411 SER SER B . n A 1 412 ILE 412 412 412 ILE ILE B . n A 1 413 PRO 413 413 413 PRO PRO B . n A 1 414 LEU 414 414 414 LEU LEU B . n A 1 415 LYS 415 415 415 LYS LYS B . n A 1 416 GLY 416 416 416 GLY GLY B . n A 1 417 ASN 417 417 417 ASN ASN B . n A 1 418 VAL 418 418 418 VAL VAL B . n A 1 419 ARG 419 419 419 ARG ARG B . n A 1 420 ASN 420 420 420 ASN ASN B . n A 1 421 LEU 421 421 421 LEU LEU B . n A 1 422 SER 422 422 422 SER SER B . n A 1 423 VAL 423 423 423 VAL VAL B . n A 1 424 LYS 424 424 424 LYS LYS B . n A 1 425 ILE 425 425 425 ILE ILE B . n A 1 426 ARG 426 426 426 ARG ARG B . n A 1 427 GLU 427 427 427 GLU GLU B . n A 1 428 CYS 428 428 428 CYS CYS B . n A 1 429 THR 429 429 429 THR THR B . n A 1 430 GLY 430 430 430 GLY GLY B . n A 1 431 LEU 431 431 431 LEU LEU B . n A 1 432 ALA 432 432 432 ALA ALA B . n A 1 433 TRP 433 433 433 TRP TRP B . n A 1 434 GLU 434 434 434 GLU GLU B . n A 1 435 TRP 435 435 435 TRP TRP B . n A 1 436 TRP 436 436 436 TRP TRP B . n A 1 437 ARG 437 437 437 ARG ARG B . n A 1 438 THR 438 438 438 THR THR B . n A 1 439 VAL 439 439 439 VAL VAL B . n A 1 440 TYR 440 440 440 TYR TYR B . n A 1 441 GLU 441 441 441 GLU GLU B . n A 1 442 LYS 442 442 442 LYS LYS B . n A 1 443 THR 443 443 443 THR THR B . n A 1 444 ASP 444 444 444 ASP ASP B . n A 1 445 LEU 445 445 445 LEU LEU B . n A 1 446 PRO 446 446 446 PRO PRO B . n A 1 447 LEU 447 447 447 LEU LEU B . n A 1 448 VAL 448 448 448 VAL VAL B . n A 1 449 ARG 449 449 449 ARG ARG B . n A 1 450 LYS 450 450 450 LYS LYS B . n A 1 451 ARG 451 451 451 ARG ARG B . n A 1 452 THR 452 452 452 THR THR B . n A 1 453 ILE 453 453 453 ILE ILE B . n A 1 454 SER 454 454 454 SER SER B . n A 1 455 ILE 455 455 455 ILE ILE B . n A 1 456 TRP 456 456 456 TRP TRP B . n A 1 457 GLY 457 457 457 GLY GLY B . n A 1 458 THR 458 458 458 THR THR B . n A 1 459 THR 459 459 459 THR THR B . n A 1 460 LEU 460 460 460 LEU LEU B . n A 1 461 TYR 461 461 461 TYR TYR B . n A 1 462 PRO 462 462 462 PRO PRO B . n A 1 463 GLN 463 463 463 GLN GLN B . n A 1 464 VAL 464 464 464 VAL VAL B . n A 1 465 GLU 465 465 465 GLU GLU B . n A 1 466 ASP 466 466 466 ASP ASP B . n A 1 467 LYS 467 467 467 LYS LYS B . n A 1 468 VAL 468 468 468 VAL VAL B . n A 1 469 GLU 469 469 469 GLU GLU B . n A 1 470 ASN 470 470 470 ASN ASN B . n A 1 471 ASP 471 471 471 ASP ASP B . n # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 0 ? 1 MORE 0 ? 1 'SSA (A^2)' 29420 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 2017-04-05 2 'Structure model' 1 1 2017-08-02 3 'Structure model' 1 2 2019-02-20 4 'Structure model' 1 3 2019-10-02 # _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 ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' Other # 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' em_image_scans 2 2 'Structure model' em_software 3 3 'Structure model' em_admin 4 3 'Structure model' pdbx_data_processing_status 5 3 'Structure model' pdbx_database_proc 6 3 'Structure model' pdbx_validate_close_contact 7 3 'Structure model' struct_conn 8 3 'Structure model' struct_conn_type 9 4 'Structure model' atom_sites 10 4 'Structure model' cell # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_em_software.name' 2 3 'Structure model' '_em_admin.last_update' 3 4 'Structure model' '_atom_sites.fract_transf_matrix[1][1]' 4 4 'Structure model' '_atom_sites.fract_transf_matrix[2][2]' 5 4 'Structure model' '_atom_sites.fract_transf_matrix[3][3]' 6 4 'Structure model' '_cell.length_a' 7 4 'Structure model' '_cell.length_b' 8 4 'Structure model' '_cell.length_c' # _em_3d_fitting.entry_id 5LY6 _em_3d_fitting.id 1 _em_3d_fitting.details ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.ref_protocol 'AB INITIO MODEL' _em_3d_fitting.ref_space ? _em_3d_fitting.target_criteria ? _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.details ? _em_3d_fitting_list.pdb_chain_id A _em_3d_fitting_list.pdb_chain_residue_range 1-471 _em_3d_fitting_list.pdb_entry_id 5AOD # _em_3d_reconstruction.entry_id 5LY6 _em_3d_reconstruction.id 1 _em_3d_reconstruction.algorithm ? _em_3d_reconstruction.details ? _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.num_particles 6461 _em_3d_reconstruction.resolution 4.5 _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_3d_reconstruction.citation_id ? _em_3d_reconstruction.euler_angles_details ? # _em_buffer.id 1 _em_buffer.details ? _em_buffer.pH 7 _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 'Pneumolysin pore complex' _em_entity_assembly.source RECOMBINANT _em_entity_assembly.type 'ORGANELLE OR CELLULAR COMPONENT' _em_entity_assembly.entity_id_list 1 _em_entity_assembly.synonym ? _em_entity_assembly.oligomeric_details ? # _em_imaging.id 1 _em_imaging.entry_id 5LY6 _em_imaging.accelerating_voltage 300 _em_imaging.alignment_procedure ? _em_imaging.c2_aperture_diameter ? _em_imaging.calibrated_defocus_max ? _em_imaging.calibrated_defocus_min ? _em_imaging.calibrated_magnification ? _em_imaging.cryogen ? _em_imaging.details ? _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.microscope_model 'FEI POLARA 300' _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_cs ? _em_imaging.nominal_defocus_max ? _em_imaging.nominal_defocus_min ? _em_imaging.nominal_magnification ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? _em_imaging.residual_tilt ? _em_imaging.specimen_holder_model ? _em_imaging.specimen_id 1 _em_imaging.date ? _em_imaging.temperature ? _em_imaging.tilt_angle_min ? _em_imaging.tilt_angle_max ? _em_imaging.specimen_holder_type ? _em_imaging.astigmatism ? _em_imaging.electron_beam_tilt_params ? _em_imaging.citation_id ? _em_imaging.detector_distance ? # _em_vitrification.id 1 _em_vitrification.specimen_id 1 _em_vitrification.chamber_temperature ? _em_vitrification.cryogen_name ETHANE _em_vitrification.details ? _em_vitrification.humidity ? _em_vitrification.instrument ? _em_vitrification.entry_id 5LY6 _em_vitrification.temp ? _em_vitrification.method ? _em_vitrification.time_resolved_state ? _em_vitrification.citation_id ? # _em_experiment.entry_id 5LY6 _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 5LY6 _em_single_particle_entity.id 1 _em_single_particle_entity.image_processing_id 1 _em_single_particle_entity.point_symmetry C42 # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 CG1 B VAL 78 ? ? CD B PRO 233 ? ? 1.53 2 1 OD2 B ASP 295 ? ? ND1 B HIS 324 ? ? 1.81 3 1 CG2 B VAL 302 ? ? CD1 B LEU 313 ? ? 1.85 4 1 N B LEU 76 ? ? O B VAL 235 ? ? 1.88 5 1 CG1 B VAL 78 ? ? CG B PRO 233 ? ? 1.89 6 1 O B TYR 236 ? ? N B SER 334 ? ? 2.02 7 1 OH B TYR 371 ? ? CD1 B ILE 455 ? ? 2.07 8 1 N B TYR 236 ? ? O B SER 334 ? ? 2.08 9 1 O B ALA 74 ? ? CB B TYR 236 ? ? 2.09 10 1 CG2 B VAL 235 ? ? CE1 B PHE 335 ? ? 2.10 11 1 CB B ARG 244 ? ? CA B GLY 293 ? ? 2.11 12 1 O B VAL 62 ? ? OG1 B THR 65 ? ? 2.11 13 1 O B ILE 60 ? ? OG1 B THR 63 ? ? 2.11 14 1 CB B PRO 233 ? ? NH2 B ARG 337 ? ? 2.12 15 1 OH B TYR 199 ? ? NE B ARG 244 ? ? 2.12 16 1 CE1 B HIS 135 ? ? CB B ALA 322 ? ? 2.16 17 1 CB B PRO 233 ? ? CZ B ARG 337 ? ? 2.18 18 1 OG1 B THR 81 ? ? CB B PRO 87 ? ? 2.18 19 1 O B LEU 161 ? ? N B HIS 184 ? ? 2.18 20 1 O B SER 58 ? ? OG B SER 61 ? ? 2.18 21 1 OG1 B THR 81 ? ? CA B PRO 87 ? ? 2.19 # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 C _pdbx_validate_rmsd_bond.auth_asym_id_1 B _pdbx_validate_rmsd_bond.auth_comp_id_1 THR _pdbx_validate_rmsd_bond.auth_seq_id_1 57 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 N _pdbx_validate_rmsd_bond.auth_asym_id_2 B _pdbx_validate_rmsd_bond.auth_comp_id_2 SER _pdbx_validate_rmsd_bond.auth_seq_id_2 58 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.597 _pdbx_validate_rmsd_bond.bond_target_value 1.336 _pdbx_validate_rmsd_bond.bond_deviation 0.261 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.023 _pdbx_validate_rmsd_bond.linker_flag Y # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 C B LEU 39 ? ? N B PRO 40 ? ? CD B PRO 40 ? ? 97.79 128.40 -30.61 2.10 Y 2 1 O B THR 57 ? ? C B THR 57 ? ? N B SER 58 ? ? 111.38 122.70 -11.32 1.60 Y 3 1 C B TYR 71 ? ? N B PRO 72 ? ? CD B PRO 72 ? ? 103.09 128.40 -25.31 2.10 Y 4 1 C B ASN 86 ? ? N B PRO 87 ? ? CD B PRO 87 ? ? 114.57 128.40 -13.83 2.10 Y 5 1 C B ASP 117 ? ? N B PRO 118 ? ? CD B PRO 118 ? ? 99.67 128.40 -28.73 2.10 Y 6 1 C B ASN 209 ? ? N B PRO 210 ? ? CD B PRO 210 ? ? 114.39 128.40 -14.01 2.10 Y 7 1 C B ALA 273 ? ? N B PRO 274 ? ? CD B PRO 274 ? ? 102.20 128.40 -26.20 2.10 Y 8 1 C B ASP 295 ? ? N B PRO 296 ? ? CD B PRO 296 ? ? 108.79 128.40 -19.61 2.10 Y 9 1 C B LEU 445 ? ? N B PRO 446 ? ? CD B PRO 446 ? ? 114.86 128.40 -13.54 2.10 Y # 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 HIS B 23 ? ? -115.79 77.00 2 1 GLU B 26 ? ? -107.08 -145.68 3 1 SER B 27 ? ? -89.35 -94.71 4 1 ILE B 33 ? ? -161.23 116.70 5 1 GLN B 38 ? ? -160.02 -23.94 6 1 LEU B 39 ? ? -91.00 -101.31 7 1 ASP B 41 ? ? -160.29 113.66 8 1 SER B 52 ? ? -160.06 -68.53 9 1 SER B 54 ? ? -71.93 -82.04 10 1 SER B 68 ? ? -109.29 63.49 11 1 ARG B 69 ? ? -99.61 38.74 12 1 LEU B 75 ? ? -152.06 83.21 13 1 ASP B 79 ? ? -138.72 -73.06 14 1 GLU B 80 ? ? -138.65 -43.10 15 1 ASN B 86 ? ? -177.51 83.71 16 1 PRO B 87 ? ? -111.80 -165.46 17 1 LEU B 89 ? ? -109.99 41.28 18 1 LEU B 103 ? ? -142.01 -150.73 19 1 LEU B 113 ? ? -127.96 -136.64 20 1 GLU B 116 ? ? -93.00 -144.27 21 1 ASN B 120 ? ? -153.93 40.52 22 1 GLN B 136 ? ? -72.85 -70.76 23 1 GLN B 140 ? ? -150.54 -99.76 24 1 VAL B 141 ? ? 49.80 -90.59 25 1 ALA B 172 ? ? -75.20 37.11 26 1 ALA B 173 ? ? -159.25 -63.93 27 1 TYR B 199 ? ? -114.09 -70.13 28 1 ALA B 206 ? ? -22.62 151.69 29 1 ASN B 209 ? ? -138.36 -152.27 30 1 GLN B 215 ? ? -92.51 -154.94 31 1 ARG B 226 ? ? -66.60 -74.83 32 1 SER B 229 ? ? -104.88 -150.77 33 1 SER B 238 ? ? -87.76 -100.07 34 1 GLN B 245 ? ? -160.21 110.61 35 1 ALA B 266 ? ? -161.56 62.14 36 1 LEU B 268 ? ? -67.93 92.78 37 1 PRO B 296 ? ? -137.24 -83.95 38 1 LYS B 306 ? ? -131.83 -99.75 39 1 VAL B 307 ? ? -131.67 -41.25 40 1 ASP B 308 ? ? -97.84 57.43 41 1 MET B 309 ? ? -99.87 -64.10 42 1 ILE B 314 ? ? -107.90 45.39 43 1 GLN B 315 ? ? -158.74 -25.94 44 1 THR B 321 ? ? -143.28 -69.64 45 1 ALA B 322 ? ? -146.44 -22.59 46 1 ILE B 329 ? ? -118.41 -79.60 47 1 ARG B 337 ? ? -153.61 -47.35 48 1 ASP B 338 ? ? -143.09 16.59 49 1 VAL B 340 ? ? -141.43 -63.82 50 1 VAL B 341 ? ? -54.72 105.20 51 1 ASN B 346 ? ? -109.41 -145.59 52 1 TYR B 376 ? ? -117.94 72.84 53 1 LEU B 382 ? ? -67.22 -166.95 54 1 SER B 383 ? ? 168.59 144.52 55 1 GLN B 387 ? ? -60.65 -71.46 56 1 ARG B 399 ? ? -108.07 68.83 57 1 GLN B 402 ? ? 176.36 153.67 58 1 THR B 410 ? ? -162.45 -163.44 59 1 SER B 411 ? ? 174.51 127.91 60 1 LEU B 414 ? ? -69.62 -154.02 61 1 LYS B 415 ? ? -177.78 87.61 62 1 ARG B 419 ? ? 176.70 125.28 63 1 ASN B 420 ? ? 75.83 144.45 64 1 LEU B 421 ? ? -160.13 105.47 65 1 LEU B 431 ? ? 49.93 -134.51 66 1 ALA B 432 ? ? -146.99 -28.66 67 1 GLU B 434 ? ? -100.51 -168.95 68 1 TRP B 435 ? ? -149.01 -44.89 69 1 VAL B 439 ? ? -81.64 -79.88 70 1 LEU B 447 ? ? -61.33 94.13 71 1 THR B 458 ? ? -106.50 -150.23 72 1 LEU B 460 ? ? -132.68 -53.03 73 1 GLN B 463 ? ? -101.25 54.80 # _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 ? _em_entity_assembly_molwt.units MEGADALTONS _em_entity_assembly_molwt.value 2.2 # _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 1313 _em_entity_assembly_naturalsource.organ . _em_entity_assembly_naturalsource.organelle ? _em_entity_assembly_naturalsource.organism 'Streptococcus pneumoniae' _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 511693 _em_entity_assembly_recombinant.organism 'Escherichia coli BL21' _em_entity_assembly_recombinant.plasmid pET15 _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 1.02 _em_image_recording.average_exposure_time 6 _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 ? _em_image_recording.num_real_images ? # 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' ? RELION 1.4 1 ? ? 2 'IMAGE ACQUISITION' ? RELION 1.4 ? ? 1 3 MASKING ? ? ? ? ? ? 4 'CTF CORRECTION' ? CTFFIND 3 1 ? ? 5 'LAYERLINE INDEXING' ? ? ? ? ? ? 6 'DIFFRACTION INDEXING' ? ? ? ? ? ? 7 'MODEL FITTING' ? Coot 8.4 ? 1 ? 8 OTHER ? ? ? ? ? ? 9 'INITIAL EULER ASSIGNMENT' ? RELION 1.4 1 ? ? 10 'FINAL EULER ASSIGNMENT' ? RELION 1.4 1 ? ? 11 CLASSIFICATION ? RELION 1.4 1 ? ? 12 RECONSTRUCTION ? RELION 1.4 1 ? ? 13 'MODEL REFINEMENT' ? Coot 8.4 ? 1 ? # _em_specimen.id 1 _em_specimen.experiment_id 1 _em_specimen.concentration 1 _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 'Max Planck Society' _pdbx_audit_support.country Germany _pdbx_audit_support.grant_number 'Biophysics/Structural Biology' _pdbx_audit_support.ordinal 1 #