data_2BK2 # _entry.id 2BK2 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2BK2 PDBE EBI-22893 WWPDB D_1290022893 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 1M3I unspecified 'PERFRINGOLYSIN O, NEW CRYSTAL FORM' PDB 1M3J unspecified 'CRYSTAL FORM II OF PERFRINGOLYSIN O' PDB 1PFO unspecified 'PERFRINGOLYSIN O' PDB 2BK1 unspecified 'THE PORE STRUCTURE OF PNEUMOLYSIN, OBTAINED BY FITTING THE ALPHA CARBON TRACE OF PERFRINGOLYSIN O INTO A CRYO-EM MAP' EMDB EMD-1106 'associated EM volume' 'THE PORE STRUCTURE OF PNEUMOLYSIN VOLUME DATA' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2BK2 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2005-02-10 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Tilley, S.J.' 1 'Orlova, E.V.' 2 'Gilbert, R.J.C.' 3 'Andrew, P.W.' 4 'Saibil, H.R.' 5 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'Structural Basis of Pore Formation by the Bacterial Toxin Pneumolysin' 'Cell(Cambridge,Mass.)' 121 247 ? 2005 CELLB5 US 0092-8674 0998 ? 15851031 10.1016/J.CELL.2005.02.033 1 'Structure of a Cholesterol-Binding, Thiol-Activated Cytolysin and a Model of its Membrane Form' 'Cell(Cambridge,Mass.)' 89 685 ? 1997 CELLB5 US 0092-8674 0998 ? 9182756 '10.1016/S0092-8674(00)80251-2' # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Tilley, S.J.' 1 primary 'Orlova, E.V.' 2 primary 'Gilbert, R.J.C.' 3 primary 'Andrew, P.W.' 4 primary 'Saibil, H.R.' 5 1 'Rossjohn, J.' 6 1 'Feil, S.C.' 7 1 'Mckinstry, W.J.' 8 1 'Tweten, R.K.' 9 1 'Parker, M.W.' 10 # _cell.entry_id 2BK2 _cell.length_a 1.000 _cell.length_b 1.000 _cell.length_c 1.000 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BK2 _symmetry.space_group_name_H-M 'P 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 # _entity.id 1 _entity.type polymer _entity.src_method man _entity.pdbx_description 'PERFRINGOLYSIN O' _entity.formula_weight 50992.805 _entity.pdbx_number_of_molecules 1 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment 'RESIDUES 36-500' _entity.details ? # _entity_name_com.entity_id 1 _entity_name_com.name 'THETA-TOXIN, 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 ;QSIDSGISSLSYNRNEVLASNGDKIESFVPKEGKKAGNKFIVVERQKRSLTTSPVDISIIDSVNDRTYPGALQLADKAFV ENRPTILMVKRKPININISIKVDDPTYGKVSGAIDELVSKWNEKYSSTHTLPARTQYSESMVYSKSQISSALNVNAKVLE NSLGVDFNAVANNEKKVMILAYKQIFYTVSADLPKNPSDLFDDSVTFNDLKQKGVSNEAPPLMVSNVAYGRTIYVKLETT SSSKDVQAAFKALIKNTDIKNSQQYKDIYENSSFTAVVLGGDAQEHNKVVTKDFDEIRKVIKDNATFSTKNPAYPISYTS VFLKDNSVAAVHNKTDYIETTSTEYSKGKINLDHSGAYVAQFEVAWDEVSYDKEGNEVLTHKTWDGNYQDKTAHYSTVIP LEANARNIRIKARECTGLAWEWWRDVISEYDVPLTNNINVSIWGTTLYPGSSITYN ; _entity_poly.pdbx_seq_one_letter_code_can ;QSIDSGISSLSYNRNEVLASNGDKIESFVPKEGKKAGNKFIVVERQKRSLTTSPVDISIIDSVNDRTYPGALQLADKAFV ENRPTILMVKRKPININISIKVDDPTYGKVSGAIDELVSKWNEKYSSTHTLPARTQYSESMVYSKSQISSALNVNAKVLE NSLGVDFNAVANNEKKVMILAYKQIFYTVSADLPKNPSDLFDDSVTFNDLKQKGVSNEAPPLMVSNVAYGRTIYVKLETT SSSKDVQAAFKALIKNTDIKNSQQYKDIYENSSFTAVVLGGDAQEHNKVVTKDFDEIRKVIKDNATFSTKNPAYPISYTS VFLKDNSVAAVHNKTDYIETTSTEYSKGKINLDHSGAYVAQFEVAWDEVSYDKEGNEVLTHKTWDGNYQDKTAHYSTVIP LEANARNIRIKARECTGLAWEWWRDVISEYDVPLTNNINVSIWGTTLYPGSSITYN ; _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 GLN n 1 2 SER n 1 3 ILE n 1 4 ASP n 1 5 SER n 1 6 GLY n 1 7 ILE n 1 8 SER n 1 9 SER n 1 10 LEU n 1 11 SER n 1 12 TYR n 1 13 ASN n 1 14 ARG n 1 15 ASN n 1 16 GLU n 1 17 VAL n 1 18 LEU n 1 19 ALA n 1 20 SER n 1 21 ASN n 1 22 GLY n 1 23 ASP n 1 24 LYS n 1 25 ILE n 1 26 GLU n 1 27 SER n 1 28 PHE n 1 29 VAL n 1 30 PRO n 1 31 LYS n 1 32 GLU n 1 33 GLY n 1 34 LYS n 1 35 LYS n 1 36 ALA n 1 37 GLY n 1 38 ASN n 1 39 LYS n 1 40 PHE n 1 41 ILE n 1 42 VAL n 1 43 VAL n 1 44 GLU n 1 45 ARG n 1 46 GLN n 1 47 LYS n 1 48 ARG n 1 49 SER n 1 50 LEU n 1 51 THR n 1 52 THR n 1 53 SER n 1 54 PRO n 1 55 VAL n 1 56 ASP n 1 57 ILE n 1 58 SER n 1 59 ILE n 1 60 ILE n 1 61 ASP n 1 62 SER n 1 63 VAL n 1 64 ASN n 1 65 ASP n 1 66 ARG n 1 67 THR n 1 68 TYR n 1 69 PRO n 1 70 GLY n 1 71 ALA n 1 72 LEU n 1 73 GLN n 1 74 LEU n 1 75 ALA n 1 76 ASP n 1 77 LYS n 1 78 ALA n 1 79 PHE n 1 80 VAL n 1 81 GLU n 1 82 ASN n 1 83 ARG n 1 84 PRO n 1 85 THR n 1 86 ILE n 1 87 LEU n 1 88 MET n 1 89 VAL n 1 90 LYS n 1 91 ARG n 1 92 LYS n 1 93 PRO n 1 94 ILE n 1 95 ASN n 1 96 ILE n 1 97 ASN n 1 98 ILE n 1 99 SER n 1 100 ILE n 1 101 LYS n 1 102 VAL n 1 103 ASP n 1 104 ASP n 1 105 PRO n 1 106 THR n 1 107 TYR n 1 108 GLY n 1 109 LYS n 1 110 VAL n 1 111 SER n 1 112 GLY n 1 113 ALA n 1 114 ILE n 1 115 ASP n 1 116 GLU n 1 117 LEU n 1 118 VAL n 1 119 SER n 1 120 LYS n 1 121 TRP n 1 122 ASN n 1 123 GLU n 1 124 LYS n 1 125 TYR n 1 126 SER n 1 127 SER n 1 128 THR n 1 129 HIS n 1 130 THR n 1 131 LEU n 1 132 PRO n 1 133 ALA n 1 134 ARG n 1 135 THR n 1 136 GLN n 1 137 TYR n 1 138 SER n 1 139 GLU n 1 140 SER n 1 141 MET n 1 142 VAL n 1 143 TYR n 1 144 SER n 1 145 LYS n 1 146 SER n 1 147 GLN n 1 148 ILE n 1 149 SER n 1 150 SER n 1 151 ALA n 1 152 LEU n 1 153 ASN n 1 154 VAL n 1 155 ASN n 1 156 ALA n 1 157 LYS n 1 158 VAL n 1 159 LEU n 1 160 GLU n 1 161 ASN n 1 162 SER n 1 163 LEU n 1 164 GLY n 1 165 VAL n 1 166 ASP n 1 167 PHE n 1 168 ASN n 1 169 ALA n 1 170 VAL n 1 171 ALA n 1 172 ASN n 1 173 ASN n 1 174 GLU n 1 175 LYS n 1 176 LYS n 1 177 VAL n 1 178 MET n 1 179 ILE n 1 180 LEU n 1 181 ALA n 1 182 TYR n 1 183 LYS n 1 184 GLN n 1 185 ILE n 1 186 PHE n 1 187 TYR n 1 188 THR n 1 189 VAL n 1 190 SER n 1 191 ALA n 1 192 ASP n 1 193 LEU n 1 194 PRO n 1 195 LYS n 1 196 ASN n 1 197 PRO n 1 198 SER n 1 199 ASP n 1 200 LEU n 1 201 PHE n 1 202 ASP n 1 203 ASP n 1 204 SER n 1 205 VAL n 1 206 THR n 1 207 PHE n 1 208 ASN n 1 209 ASP n 1 210 LEU n 1 211 LYS n 1 212 GLN n 1 213 LYS n 1 214 GLY n 1 215 VAL n 1 216 SER n 1 217 ASN n 1 218 GLU n 1 219 ALA n 1 220 PRO n 1 221 PRO n 1 222 LEU n 1 223 MET n 1 224 VAL n 1 225 SER n 1 226 ASN n 1 227 VAL n 1 228 ALA n 1 229 TYR n 1 230 GLY n 1 231 ARG n 1 232 THR n 1 233 ILE n 1 234 TYR n 1 235 VAL n 1 236 LYS n 1 237 LEU n 1 238 GLU n 1 239 THR n 1 240 THR n 1 241 SER n 1 242 SER n 1 243 SER n 1 244 LYS n 1 245 ASP n 1 246 VAL n 1 247 GLN n 1 248 ALA n 1 249 ALA n 1 250 PHE n 1 251 LYS n 1 252 ALA n 1 253 LEU n 1 254 ILE n 1 255 LYS n 1 256 ASN n 1 257 THR n 1 258 ASP n 1 259 ILE n 1 260 LYS n 1 261 ASN n 1 262 SER n 1 263 GLN n 1 264 GLN n 1 265 TYR n 1 266 LYS n 1 267 ASP n 1 268 ILE n 1 269 TYR n 1 270 GLU n 1 271 ASN n 1 272 SER n 1 273 SER n 1 274 PHE n 1 275 THR n 1 276 ALA n 1 277 VAL n 1 278 VAL n 1 279 LEU n 1 280 GLY n 1 281 GLY n 1 282 ASP n 1 283 ALA n 1 284 GLN n 1 285 GLU n 1 286 HIS n 1 287 ASN n 1 288 LYS n 1 289 VAL n 1 290 VAL n 1 291 THR n 1 292 LYS n 1 293 ASP n 1 294 PHE n 1 295 ASP n 1 296 GLU n 1 297 ILE n 1 298 ARG n 1 299 LYS n 1 300 VAL n 1 301 ILE n 1 302 LYS n 1 303 ASP n 1 304 ASN n 1 305 ALA n 1 306 THR n 1 307 PHE n 1 308 SER n 1 309 THR n 1 310 LYS n 1 311 ASN n 1 312 PRO n 1 313 ALA n 1 314 TYR n 1 315 PRO n 1 316 ILE n 1 317 SER n 1 318 TYR n 1 319 THR n 1 320 SER n 1 321 VAL n 1 322 PHE n 1 323 LEU n 1 324 LYS n 1 325 ASP n 1 326 ASN n 1 327 SER n 1 328 VAL n 1 329 ALA n 1 330 ALA n 1 331 VAL n 1 332 HIS n 1 333 ASN n 1 334 LYS n 1 335 THR n 1 336 ASP n 1 337 TYR n 1 338 ILE n 1 339 GLU n 1 340 THR n 1 341 THR n 1 342 SER n 1 343 THR n 1 344 GLU n 1 345 TYR n 1 346 SER n 1 347 LYS n 1 348 GLY n 1 349 LYS n 1 350 ILE n 1 351 ASN n 1 352 LEU n 1 353 ASP n 1 354 HIS n 1 355 SER n 1 356 GLY n 1 357 ALA n 1 358 TYR n 1 359 VAL n 1 360 ALA n 1 361 GLN n 1 362 PHE n 1 363 GLU n 1 364 VAL n 1 365 ALA n 1 366 TRP n 1 367 ASP n 1 368 GLU n 1 369 VAL n 1 370 SER n 1 371 TYR n 1 372 ASP n 1 373 LYS n 1 374 GLU n 1 375 GLY n 1 376 ASN n 1 377 GLU n 1 378 VAL n 1 379 LEU n 1 380 THR n 1 381 HIS n 1 382 LYS n 1 383 THR n 1 384 TRP n 1 385 ASP n 1 386 GLY n 1 387 ASN n 1 388 TYR n 1 389 GLN n 1 390 ASP n 1 391 LYS n 1 392 THR n 1 393 ALA n 1 394 HIS n 1 395 TYR n 1 396 SER n 1 397 THR n 1 398 VAL n 1 399 ILE n 1 400 PRO n 1 401 LEU n 1 402 GLU n 1 403 ALA n 1 404 ASN n 1 405 ALA n 1 406 ARG n 1 407 ASN n 1 408 ILE n 1 409 ARG n 1 410 ILE n 1 411 LYS n 1 412 ALA n 1 413 ARG n 1 414 GLU n 1 415 CYS n 1 416 THR n 1 417 GLY n 1 418 LEU n 1 419 ALA n 1 420 TRP n 1 421 GLU n 1 422 TRP n 1 423 TRP n 1 424 ARG n 1 425 ASP n 1 426 VAL n 1 427 ILE n 1 428 SER n 1 429 GLU n 1 430 TYR n 1 431 ASP n 1 432 VAL n 1 433 PRO n 1 434 LEU n 1 435 THR n 1 436 ASN n 1 437 ASN n 1 438 ILE n 1 439 ASN n 1 440 VAL n 1 441 SER n 1 442 ILE n 1 443 TRP n 1 444 GLY n 1 445 THR n 1 446 THR n 1 447 LEU n 1 448 TYR n 1 449 PRO n 1 450 GLY n 1 451 SER n 1 452 SER n 1 453 ILE n 1 454 THR n 1 455 TYR n 1 456 ASN 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 ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene ? _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 'CLOSTRIDIUM PERFRINGENS' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1502 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'ESCHERICHIA COLI' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TACY_CLOPE _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_db_accession P19995 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2BK2 _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 456 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P19995 _struct_ref_seq.db_align_beg 36 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 500 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 36 _struct_ref_seq.pdbx_auth_seq_align_end 500 # 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.entry_id 2BK2 _exptl.method 'ELECTRON MICROSCOPY' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l ? _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol ? _diffrn_radiation.pdbx_scattering_type ? # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _refine.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine.entry_id 2BK2 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high 28.00 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_B ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'ELECTRON MICROSCOPY' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 456 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 456 _refine_hist.d_res_high 28.00 _refine_hist.d_res_low . # _struct.entry_id 2BK2 _struct.title 'The prepore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map' _struct.pdbx_descriptor 'PERFRINGOLYSIN O' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details 'CA ATOMS ONLY, CHAIN A' # _struct_keywords.entry_id 2BK2 _struct_keywords.pdbx_keywords TOXIN _struct_keywords.text 'CYTOLYSIS, HEMOLYSIS, THIOL-ACTIVATED CYTOLYSIN, TOXIN, CRYOEM, CYTOLYTIC PROTEIN' # _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_biol.id 1 # _database_PDB_matrix.entry_id 2BK2 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 2BK2 _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_type.symbol C # 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 GLN 1 36 36 GLN GLN A . n A 1 2 SER 2 37 37 SER SER A . n A 1 3 ILE 3 38 38 ILE ILE A . n A 1 4 ASP 4 39 39 ASP ASP A . n A 1 5 SER 5 40 40 SER SER A . n A 1 6 GLY 6 41 41 GLY GLY A . n A 1 7 ILE 7 42 42 ILE ILE A . n A 1 8 SER 8 43 43 SER SER A . n A 1 9 SER 9 44 44 SER SER A . n A 1 10 LEU 10 45 45 LEU LEU A . n A 1 11 SER 11 46 46 SER SER A . n A 1 12 TYR 12 47 47 TYR TYR A . n A 1 13 ASN 13 48 48 ASN ASN A . n A 1 14 ARG 14 49 49 ARG ARG A . n A 1 15 ASN 15 50 50 ASN ASN A . n A 1 16 GLU 16 51 51 GLU GLU A . n A 1 17 VAL 17 52 52 VAL VAL A . n A 1 18 LEU 18 53 53 LEU LEU A . n A 1 19 ALA 19 54 54 ALA ALA A . n A 1 20 SER 20 55 55 SER SER A . n A 1 21 ASN 21 56 56 ASN ASN A . n A 1 22 GLY 22 57 57 GLY GLY A . n A 1 23 ASP 23 58 58 ASP ASP A . n A 1 24 LYS 24 59 59 LYS LYS A . n A 1 25 ILE 25 60 60 ILE ILE A . n A 1 26 GLU 26 61 61 GLU GLU A . n A 1 27 SER 27 62 62 SER SER A . n A 1 28 PHE 28 63 63 PHE PHE A . n A 1 29 VAL 29 64 64 VAL VAL A . n A 1 30 PRO 30 65 65 PRO PRO A . n A 1 31 LYS 31 66 66 LYS LYS A . n A 1 32 GLU 32 67 67 GLU GLU A . n A 1 33 GLY 33 68 68 GLY GLY A . n A 1 34 LYS 34 69 69 LYS LYS A . n A 1 35 LYS 35 70 70 LYS LYS A . n A 1 36 ALA 36 71 71 ALA ALA A . n A 1 37 GLY 37 72 72 GLY GLY A . n A 1 38 ASN 38 73 73 ASN ASN A . n A 1 39 LYS 39 74 74 LYS LYS A . n A 1 40 PHE 40 75 75 PHE PHE A . n A 1 41 ILE 41 76 76 ILE ILE A . n A 1 42 VAL 42 77 77 VAL VAL A . n A 1 43 VAL 43 78 78 VAL VAL A . n A 1 44 GLU 44 79 79 GLU GLU A . n A 1 45 ARG 45 80 80 ARG ARG A . n A 1 46 GLN 46 81 81 GLN GLN A . n A 1 47 LYS 47 82 82 LYS LYS A . n A 1 48 ARG 48 83 83 ARG ARG A . n A 1 49 SER 49 84 84 SER SER A . n A 1 50 LEU 50 85 85 LEU LEU A . n A 1 51 THR 51 86 86 THR THR A . n A 1 52 THR 52 87 87 THR THR A . n A 1 53 SER 53 88 88 SER SER A . n A 1 54 PRO 54 89 89 PRO PRO A . n A 1 55 VAL 55 90 90 VAL VAL A . n A 1 56 ASP 56 91 91 ASP ASP A . n A 1 57 ILE 57 92 92 ILE ILE A . n A 1 58 SER 58 93 93 SER SER A . n A 1 59 ILE 59 94 94 ILE ILE A . n A 1 60 ILE 60 95 95 ILE ILE A . n A 1 61 ASP 61 96 96 ASP ASP A . n A 1 62 SER 62 97 97 SER SER A . n A 1 63 VAL 63 98 98 VAL VAL A . n A 1 64 ASN 64 99 99 ASN ASN A . n A 1 65 ASP 65 100 100 ASP ASP A . n A 1 66 ARG 66 101 101 ARG ARG A . n A 1 67 THR 67 102 102 THR THR A . n A 1 68 TYR 68 103 103 TYR TYR A . n A 1 69 PRO 69 104 104 PRO PRO A . n A 1 70 GLY 70 105 105 GLY GLY A . n A 1 71 ALA 71 106 106 ALA ALA A . n A 1 72 LEU 72 107 107 LEU LEU A . n A 1 73 GLN 73 108 108 GLN GLN A . n A 1 74 LEU 74 109 109 LEU LEU A . n A 1 75 ALA 75 110 110 ALA ALA A . n A 1 76 ASP 76 111 111 ASP ASP A . n A 1 77 LYS 77 112 112 LYS LYS A . n A 1 78 ALA 78 113 113 ALA ALA A . n A 1 79 PHE 79 114 114 PHE PHE A . n A 1 80 VAL 80 115 115 VAL VAL A . n A 1 81 GLU 81 116 116 GLU GLU A . n A 1 82 ASN 82 117 117 ASN ASN A . n A 1 83 ARG 83 118 118 ARG ARG A . n A 1 84 PRO 84 119 119 PRO PRO A . n A 1 85 THR 85 120 120 THR THR A . n A 1 86 ILE 86 121 121 ILE ILE A . n A 1 87 LEU 87 122 122 LEU LEU A . n A 1 88 MET 88 123 123 MET MET A . n A 1 89 VAL 89 124 124 VAL VAL A . n A 1 90 LYS 90 125 125 LYS LYS A . n A 1 91 ARG 91 126 126 ARG ARG A . n A 1 92 LYS 92 127 127 LYS LYS A . n A 1 93 PRO 93 128 128 PRO PRO A . n A 1 94 ILE 94 129 129 ILE ILE A . n A 1 95 ASN 95 130 130 ASN ASN A . n A 1 96 ILE 96 131 131 ILE ILE A . n A 1 97 ASN 97 132 132 ASN ASN A . n A 1 98 ILE 98 133 133 ILE ILE A . n A 1 99 SER 99 143 143 SER SER A . n A 1 100 ILE 100 144 144 ILE ILE A . n A 1 101 LYS 101 145 145 LYS LYS A . n A 1 102 VAL 102 146 146 VAL VAL A . n A 1 103 ASP 103 147 147 ASP ASP A . n A 1 104 ASP 104 148 148 ASP ASP A . n A 1 105 PRO 105 149 149 PRO PRO A . n A 1 106 THR 106 150 150 THR THR A . n A 1 107 TYR 107 151 151 TYR TYR A . n A 1 108 GLY 108 152 152 GLY GLY A . n A 1 109 LYS 109 153 153 LYS LYS A . n A 1 110 VAL 110 154 154 VAL VAL A . n A 1 111 SER 111 155 155 SER SER A . n A 1 112 GLY 112 156 156 GLY GLY A . n A 1 113 ALA 113 157 157 ALA ALA A . n A 1 114 ILE 114 158 158 ILE ILE A . n A 1 115 ASP 115 159 159 ASP ASP A . n A 1 116 GLU 116 160 160 GLU GLU A . n A 1 117 LEU 117 161 161 LEU LEU A . n A 1 118 VAL 118 162 162 VAL VAL A . n A 1 119 SER 119 163 163 SER SER A . n A 1 120 LYS 120 164 164 LYS LYS A . n A 1 121 TRP 121 165 165 TRP TRP A . n A 1 122 ASN 122 166 166 ASN ASN A . n A 1 123 GLU 123 167 167 GLU GLU A . n A 1 124 LYS 124 168 168 LYS LYS A . n A 1 125 TYR 125 169 169 TYR TYR A . n A 1 126 SER 126 170 170 SER SER A . n A 1 127 SER 127 171 171 SER SER A . n A 1 128 THR 128 172 172 THR THR A . n A 1 129 HIS 129 173 173 HIS HIS A . n A 1 130 THR 130 174 174 THR THR A . n A 1 131 LEU 131 175 175 LEU LEU A . n A 1 132 PRO 132 176 176 PRO PRO A . n A 1 133 ALA 133 177 177 ALA ALA A . n A 1 134 ARG 134 178 178 ARG ARG A . n A 1 135 THR 135 179 179 THR THR A . n A 1 136 GLN 136 180 180 GLN GLN A . n A 1 137 TYR 137 181 181 TYR TYR A . n A 1 138 SER 138 182 182 SER SER A . n A 1 139 GLU 139 183 183 GLU GLU A . n A 1 140 SER 140 184 184 SER SER A . n A 1 141 MET 141 185 185 MET MET A . n A 1 142 VAL 142 186 186 VAL VAL A . n A 1 143 TYR 143 187 187 TYR TYR A . n A 1 144 SER 144 188 188 SER SER A . n A 1 145 LYS 145 189 189 LYS LYS A . n A 1 146 SER 146 190 190 SER SER A . n A 1 147 GLN 147 191 191 GLN GLN A . n A 1 148 ILE 148 192 192 ILE ILE A . n A 1 149 SER 149 193 193 SER SER A . n A 1 150 SER 150 194 194 SER SER A . n A 1 151 ALA 151 195 195 ALA ALA A . n A 1 152 LEU 152 196 196 LEU LEU A . n A 1 153 ASN 153 197 197 ASN ASN A . n A 1 154 VAL 154 198 198 VAL VAL A . n A 1 155 ASN 155 199 199 ASN ASN A . n A 1 156 ALA 156 200 200 ALA ALA A . n A 1 157 LYS 157 201 201 LYS LYS A . n A 1 158 VAL 158 202 202 VAL VAL A . n A 1 159 LEU 159 203 203 LEU LEU A . n A 1 160 GLU 160 204 204 GLU GLU A . n A 1 161 ASN 161 205 205 ASN ASN A . n A 1 162 SER 162 206 206 SER SER A . n A 1 163 LEU 163 207 207 LEU LEU A . n A 1 164 GLY 164 208 208 GLY GLY A . n A 1 165 VAL 165 209 209 VAL VAL A . n A 1 166 ASP 166 210 210 ASP ASP A . n A 1 167 PHE 167 211 211 PHE PHE A . n A 1 168 ASN 168 212 212 ASN ASN A . n A 1 169 ALA 169 213 213 ALA ALA A . n A 1 170 VAL 170 214 214 VAL VAL A . n A 1 171 ALA 171 215 215 ALA ALA A . n A 1 172 ASN 172 216 216 ASN ASN A . n A 1 173 ASN 173 217 217 ASN ASN A . n A 1 174 GLU 174 218 218 GLU GLU A . n A 1 175 LYS 175 219 219 LYS LYS A . n A 1 176 LYS 176 220 220 LYS LYS A . n A 1 177 VAL 177 221 221 VAL VAL A . n A 1 178 MET 178 222 222 MET MET A . n A 1 179 ILE 179 223 223 ILE ILE A . n A 1 180 LEU 180 224 224 LEU LEU A . n A 1 181 ALA 181 225 225 ALA ALA A . n A 1 182 TYR 182 226 226 TYR TYR A . n A 1 183 LYS 183 227 227 LYS LYS A . n A 1 184 GLN 184 228 228 GLN GLN A . n A 1 185 ILE 185 229 229 ILE ILE A . n A 1 186 PHE 186 230 230 PHE PHE A . n A 1 187 TYR 187 231 231 TYR TYR A . n A 1 188 THR 188 232 232 THR THR A . n A 1 189 VAL 189 233 233 VAL VAL A . n A 1 190 SER 190 234 234 SER SER A . n A 1 191 ALA 191 235 235 ALA ALA A . n A 1 192 ASP 192 236 236 ASP ASP A . n A 1 193 LEU 193 237 237 LEU LEU A . n A 1 194 PRO 194 238 238 PRO PRO A . n A 1 195 LYS 195 239 239 LYS LYS A . n A 1 196 ASN 196 240 240 ASN ASN A . n A 1 197 PRO 197 241 241 PRO PRO A . n A 1 198 SER 198 242 242 SER SER A . n A 1 199 ASP 199 243 243 ASP ASP A . n A 1 200 LEU 200 244 244 LEU LEU A . n A 1 201 PHE 201 245 245 PHE PHE A . n A 1 202 ASP 202 246 246 ASP ASP A . n A 1 203 ASP 203 247 247 ASP ASP A . n A 1 204 SER 204 248 248 SER SER A . n A 1 205 VAL 205 249 249 VAL VAL A . n A 1 206 THR 206 250 250 THR THR A . n A 1 207 PHE 207 251 251 PHE PHE A . n A 1 208 ASN 208 252 252 ASN ASN A . n A 1 209 ASP 209 253 253 ASP ASP A . n A 1 210 LEU 210 254 254 LEU LEU A . n A 1 211 LYS 211 255 255 LYS LYS A . n A 1 212 GLN 212 256 256 GLN GLN A . n A 1 213 LYS 213 257 257 LYS LYS A . n A 1 214 GLY 214 258 258 GLY GLY A . n A 1 215 VAL 215 259 259 VAL VAL A . n A 1 216 SER 216 260 260 SER SER A . n A 1 217 ASN 217 261 261 ASN ASN A . n A 1 218 GLU 218 262 262 GLU GLU A . n A 1 219 ALA 219 263 263 ALA ALA A . n A 1 220 PRO 220 264 264 PRO PRO A . n A 1 221 PRO 221 265 265 PRO PRO A . n A 1 222 LEU 222 266 266 LEU LEU A . n A 1 223 MET 223 267 267 MET MET A . n A 1 224 VAL 224 268 268 VAL VAL A . n A 1 225 SER 225 269 269 SER SER A . n A 1 226 ASN 226 270 270 ASN ASN A . n A 1 227 VAL 227 271 271 VAL VAL A . n A 1 228 ALA 228 272 272 ALA ALA A . n A 1 229 TYR 229 273 273 TYR TYR A . n A 1 230 GLY 230 274 274 GLY GLY A . n A 1 231 ARG 231 275 275 ARG ARG A . n A 1 232 THR 232 276 276 THR THR A . n A 1 233 ILE 233 277 277 ILE ILE A . n A 1 234 TYR 234 278 278 TYR TYR A . n A 1 235 VAL 235 279 279 VAL VAL A . n A 1 236 LYS 236 280 280 LYS LYS A . n A 1 237 LEU 237 281 281 LEU LEU A . n A 1 238 GLU 238 282 282 GLU GLU A . n A 1 239 THR 239 283 283 THR THR A . n A 1 240 THR 240 284 284 THR THR A . n A 1 241 SER 241 285 285 SER SER A . n A 1 242 SER 242 286 286 SER SER A . n A 1 243 SER 243 287 287 SER SER A . n A 1 244 LYS 244 288 288 LYS LYS A . n A 1 245 ASP 245 289 289 ASP ASP A . n A 1 246 VAL 246 290 290 VAL VAL A . n A 1 247 GLN 247 291 291 GLN GLN A . n A 1 248 ALA 248 292 292 ALA ALA A . n A 1 249 ALA 249 293 293 ALA ALA A . n A 1 250 PHE 250 294 294 PHE PHE A . n A 1 251 LYS 251 295 295 LYS LYS A . n A 1 252 ALA 252 296 296 ALA ALA A . n A 1 253 LEU 253 297 297 LEU LEU A . n A 1 254 ILE 254 298 298 ILE ILE A . n A 1 255 LYS 255 299 299 LYS LYS A . n A 1 256 ASN 256 300 300 ASN ASN A . n A 1 257 THR 257 301 301 THR THR A . n A 1 258 ASP 258 302 302 ASP ASP A . n A 1 259 ILE 259 303 303 ILE ILE A . n A 1 260 LYS 260 304 304 LYS LYS A . n A 1 261 ASN 261 305 305 ASN ASN A . n A 1 262 SER 262 306 306 SER SER A . n A 1 263 GLN 263 307 307 GLN GLN A . n A 1 264 GLN 264 308 308 GLN GLN A . n A 1 265 TYR 265 309 309 TYR TYR A . n A 1 266 LYS 266 310 310 LYS LYS A . n A 1 267 ASP 267 311 311 ASP ASP A . n A 1 268 ILE 268 312 312 ILE ILE A . n A 1 269 TYR 269 313 313 TYR TYR A . n A 1 270 GLU 270 314 314 GLU GLU A . n A 1 271 ASN 271 315 315 ASN ASN A . n A 1 272 SER 272 316 316 SER SER A . n A 1 273 SER 273 317 317 SER SER A . n A 1 274 PHE 274 318 318 PHE PHE A . n A 1 275 THR 275 319 319 THR THR A . n A 1 276 ALA 276 320 320 ALA ALA A . n A 1 277 VAL 277 321 321 VAL VAL A . n A 1 278 VAL 278 322 322 VAL VAL A . n A 1 279 LEU 279 323 323 LEU LEU A . n A 1 280 GLY 280 324 324 GLY GLY A . n A 1 281 GLY 281 325 325 GLY GLY A . n A 1 282 ASP 282 326 326 ASP ASP A . n A 1 283 ALA 283 327 327 ALA ALA A . n A 1 284 GLN 284 328 328 GLN GLN A . n A 1 285 GLU 285 329 329 GLU GLU A . n A 1 286 HIS 286 330 330 HIS HIS A . n A 1 287 ASN 287 331 331 ASN ASN A . n A 1 288 LYS 288 332 332 LYS LYS A . n A 1 289 VAL 289 333 333 VAL VAL A . n A 1 290 VAL 290 334 334 VAL VAL A . n A 1 291 THR 291 335 335 THR THR A . n A 1 292 LYS 292 336 336 LYS LYS A . n A 1 293 ASP 293 337 337 ASP ASP A . n A 1 294 PHE 294 338 338 PHE PHE A . n A 1 295 ASP 295 339 339 ASP ASP A . n A 1 296 GLU 296 340 340 GLU GLU A . n A 1 297 ILE 297 341 341 ILE ILE A . n A 1 298 ARG 298 342 342 ARG ARG A . n A 1 299 LYS 299 343 343 LYS LYS A . n A 1 300 VAL 300 344 344 VAL VAL A . n A 1 301 ILE 301 345 345 ILE ILE A . n A 1 302 LYS 302 346 346 LYS LYS A . n A 1 303 ASP 303 347 347 ASP ASP A . n A 1 304 ASN 304 348 348 ASN ASN A . n A 1 305 ALA 305 349 349 ALA ALA A . n A 1 306 THR 306 350 350 THR THR A . n A 1 307 PHE 307 351 351 PHE PHE A . n A 1 308 SER 308 352 352 SER SER A . n A 1 309 THR 309 353 353 THR THR A . n A 1 310 LYS 310 354 354 LYS LYS A . n A 1 311 ASN 311 355 355 ASN ASN A . n A 1 312 PRO 312 356 356 PRO PRO A . n A 1 313 ALA 313 357 357 ALA ALA A . n A 1 314 TYR 314 358 358 TYR TYR A . n A 1 315 PRO 315 359 359 PRO PRO A . n A 1 316 ILE 316 360 360 ILE ILE A . n A 1 317 SER 317 361 361 SER SER A . n A 1 318 TYR 318 362 362 TYR TYR A . n A 1 319 THR 319 363 363 THR THR A . n A 1 320 SER 320 364 364 SER SER A . n A 1 321 VAL 321 365 365 VAL VAL A . n A 1 322 PHE 322 366 366 PHE PHE A . n A 1 323 LEU 323 367 367 LEU LEU A . n A 1 324 LYS 324 368 368 LYS LYS A . n A 1 325 ASP 325 369 369 ASP ASP A . n A 1 326 ASN 326 370 370 ASN ASN A . n A 1 327 SER 327 371 371 SER SER A . n A 1 328 VAL 328 372 372 VAL VAL A . n A 1 329 ALA 329 373 373 ALA ALA A . n A 1 330 ALA 330 374 374 ALA ALA A . n A 1 331 VAL 331 375 375 VAL VAL A . n A 1 332 HIS 332 376 376 HIS HIS A . n A 1 333 ASN 333 377 377 ASN ASN A . n A 1 334 LYS 334 378 378 LYS LYS A . n A 1 335 THR 335 379 379 THR THR A . n A 1 336 ASP 336 380 380 ASP ASP A . n A 1 337 TYR 337 381 381 TYR TYR A . n A 1 338 ILE 338 382 382 ILE ILE A . n A 1 339 GLU 339 383 383 GLU GLU A . n A 1 340 THR 340 384 384 THR THR A . n A 1 341 THR 341 385 385 THR THR A . n A 1 342 SER 342 386 386 SER SER A . n A 1 343 THR 343 387 387 THR THR A . n A 1 344 GLU 344 388 388 GLU GLU A . n A 1 345 TYR 345 389 389 TYR TYR A . n A 1 346 SER 346 390 390 SER SER A . n A 1 347 LYS 347 391 391 LYS LYS A . n A 1 348 GLY 348 392 392 GLY GLY A . n A 1 349 LYS 349 393 393 LYS LYS A . n A 1 350 ILE 350 394 394 ILE ILE A . n A 1 351 ASN 351 395 395 ASN ASN A . n A 1 352 LEU 352 396 396 LEU LEU A . n A 1 353 ASP 353 397 397 ASP ASP A . n A 1 354 HIS 354 398 398 HIS HIS A . n A 1 355 SER 355 399 399 SER SER A . n A 1 356 GLY 356 400 400 GLY GLY A . n A 1 357 ALA 357 401 401 ALA ALA A . n A 1 358 TYR 358 402 402 TYR TYR A . n A 1 359 VAL 359 403 403 VAL VAL A . n A 1 360 ALA 360 404 404 ALA ALA A . n A 1 361 GLN 361 405 405 GLN GLN A . n A 1 362 PHE 362 406 406 PHE PHE A . n A 1 363 GLU 363 407 407 GLU GLU A . n A 1 364 VAL 364 408 408 VAL VAL A . n A 1 365 ALA 365 409 409 ALA ALA A . n A 1 366 TRP 366 410 410 TRP TRP A . n A 1 367 ASP 367 411 411 ASP ASP A . n A 1 368 GLU 368 412 412 GLU GLU A . n A 1 369 VAL 369 413 413 VAL VAL A . n A 1 370 SER 370 414 414 SER SER A . n A 1 371 TYR 371 415 415 TYR TYR A . n A 1 372 ASP 372 416 416 ASP ASP A . n A 1 373 LYS 373 417 417 LYS LYS A . n A 1 374 GLU 374 418 418 GLU GLU A . n A 1 375 GLY 375 419 419 GLY GLY A . n A 1 376 ASN 376 420 420 ASN ASN A . n A 1 377 GLU 377 421 421 GLU GLU A . n A 1 378 VAL 378 422 422 VAL VAL A . n A 1 379 LEU 379 423 423 LEU LEU A . n A 1 380 THR 380 424 424 THR THR A . n A 1 381 HIS 381 425 425 HIS HIS A . n A 1 382 LYS 382 426 426 LYS LYS A . n A 1 383 THR 383 427 427 THR THR A . n A 1 384 TRP 384 428 428 TRP TRP A . n A 1 385 ASP 385 429 429 ASP ASP A . n A 1 386 GLY 386 430 430 GLY GLY A . n A 1 387 ASN 387 431 431 ASN ASN A . n A 1 388 TYR 388 432 432 TYR TYR A . n A 1 389 GLN 389 433 433 GLN GLN A . n A 1 390 ASP 390 434 434 ASP ASP A . n A 1 391 LYS 391 435 435 LYS LYS A . n A 1 392 THR 392 436 436 THR THR A . n A 1 393 ALA 393 437 437 ALA ALA A . n A 1 394 HIS 394 438 438 HIS HIS A . n A 1 395 TYR 395 439 439 TYR TYR A . n A 1 396 SER 396 440 440 SER SER A . n A 1 397 THR 397 441 441 THR THR A . n A 1 398 VAL 398 442 442 VAL VAL A . n A 1 399 ILE 399 443 443 ILE ILE A . n A 1 400 PRO 400 444 444 PRO PRO A . n A 1 401 LEU 401 445 445 LEU LEU A . n A 1 402 GLU 402 446 446 GLU GLU A . n A 1 403 ALA 403 447 447 ALA ALA A . n A 1 404 ASN 404 448 448 ASN ASN A . n A 1 405 ALA 405 449 449 ALA ALA A . n A 1 406 ARG 406 450 450 ARG ARG A . n A 1 407 ASN 407 451 451 ASN ASN A . n A 1 408 ILE 408 452 452 ILE ILE A . n A 1 409 ARG 409 453 453 ARG ARG A . n A 1 410 ILE 410 454 454 ILE ILE A . n A 1 411 LYS 411 455 455 LYS LYS A . n A 1 412 ALA 412 456 456 ALA ALA A . n A 1 413 ARG 413 457 457 ARG ARG A . n A 1 414 GLU 414 458 458 GLU GLU A . n A 1 415 CYS 415 459 459 CYS CYS A . n A 1 416 THR 416 460 460 THR THR A . n A 1 417 GLY 417 461 461 GLY GLY A . n A 1 418 LEU 418 462 462 LEU LEU A . n A 1 419 ALA 419 463 463 ALA ALA A . n A 1 420 TRP 420 464 464 TRP TRP A . n A 1 421 GLU 421 465 465 GLU GLU A . n A 1 422 TRP 422 466 466 TRP TRP A . n A 1 423 TRP 423 467 467 TRP TRP A . n A 1 424 ARG 424 468 468 ARG ARG A . n A 1 425 ASP 425 469 469 ASP ASP A . n A 1 426 VAL 426 470 470 VAL VAL A . n A 1 427 ILE 427 471 471 ILE ILE A . n A 1 428 SER 428 472 472 SER SER A . n A 1 429 GLU 429 473 473 GLU GLU A . n A 1 430 TYR 430 474 474 TYR TYR A . n A 1 431 ASP 431 475 475 ASP ASP A . n A 1 432 VAL 432 476 476 VAL VAL A . n A 1 433 PRO 433 477 477 PRO PRO A . n A 1 434 LEU 434 478 478 LEU LEU A . n A 1 435 THR 435 479 479 THR THR A . n A 1 436 ASN 436 480 480 ASN ASN A . n A 1 437 ASN 437 481 481 ASN ASN A . n A 1 438 ILE 438 482 482 ILE ILE A . n A 1 439 ASN 439 483 483 ASN ASN A . n A 1 440 VAL 440 484 484 VAL VAL A . n A 1 441 SER 441 485 485 SER SER A . n A 1 442 ILE 442 486 486 ILE ILE A . n A 1 443 TRP 443 487 487 TRP TRP A . n A 1 444 GLY 444 488 488 GLY GLY A . n A 1 445 THR 445 489 489 THR THR A . n A 1 446 THR 446 490 490 THR THR A . n A 1 447 LEU 447 491 491 LEU LEU A . n A 1 448 TYR 448 492 492 TYR TYR A . n A 1 449 PRO 449 493 493 PRO PRO A . n A 1 450 GLY 450 494 494 GLY GLY A . n A 1 451 SER 451 495 495 SER SER A . n A 1 452 SER 452 496 496 SER SER A . n A 1 453 ILE 453 497 497 ILE ILE A . n A 1 454 THR 454 498 498 THR THR A . n A 1 455 TYR 455 499 499 TYR TYR A . n A 1 456 ASN 456 500 500 ASN ASN A . n # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 'complete point assembly' ? 31-MERIC 31 2 'point asymmetric unit' ? monomeric 1 3 'point asymmetric unit, std point frame' ? monomeric 1 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 '(1-31)' A 2 1 A 3 P A # 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' ? ? -0.02676384 0.99964178 0.00000000 0.00000 -0.99964178 -0.02676384 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 -41.91250 1 'point symmetry operation' ? ? 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' ? ? 0.97952994 -0.20129852 0.00000000 0.00000 0.20129852 0.97952994 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 3 'point symmetry operation' ? ? 0.91895781 -0.39435586 0.00000000 0.00000 0.39435586 0.91895781 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 4 'point symmetry operation' ? ? 0.82076344 -0.57126822 0.00000000 0.00000 0.57126822 0.82076344 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 5 'point symmetry operation' ? ? 0.68896692 -0.72479279 0.00000000 0.00000 0.72479279 0.68896692 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 6 'point symmetry operation' ? ? 0.52896401 -0.84864426 0.00000000 0.00000 0.84864426 0.52896401 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 7 'point symmetry operation' ? ? 0.34730525 -0.93775213 0.00000000 0.00000 0.93775213 0.34730525 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 8 'point symmetry operation' ? ? 0.15142778 -0.98846832 0.00000000 0.00000 0.98846832 0.15142778 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 9 'point symmetry operation' ? ? -0.05064917 -0.99871651 0.00000000 0.00000 0.99871651 -0.05064917 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 10 'point symmetry operation' ? ? -0.25065253 -0.96807712 0.00000000 0.00000 0.96807712 -0.25065253 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 11 'point symmetry operation' ? ? -0.44039415 -0.89780454 0.00000000 0.00000 0.89780454 -0.44039415 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 12 'point symmetry operation' ? ? -0.61210598 -0.79077574 0.00000000 0.00000 0.79077574 -0.61210598 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 13 'point symmetry operation' ? ? -0.75875812 -0.65137248 0.00000000 0.00000 0.65137248 -0.75875812 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 14 'point symmetry operation' ? ? -0.87434662 -0.48530196 0.00000000 0.00000 0.48530196 -0.87434662 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 15 'point symmetry operation' ? ? -0.95413926 -0.29936312 0.00000000 0.00000 0.29936312 -0.95413926 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 16 'point symmetry operation' ? ? -0.99486932 -0.10116832 0.00000000 0.00000 0.10116832 -0.99486932 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 17 'point symmetry operation' ? ? -0.99486932 0.10116832 0.00000000 0.00000 -0.10116832 -0.99486932 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 18 'point symmetry operation' ? ? -0.95413926 0.29936312 0.00000000 0.00000 -0.29936312 -0.95413926 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 19 'point symmetry operation' ? ? -0.87434662 0.48530196 0.00000000 0.00000 -0.48530196 -0.87434662 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 20 'point symmetry operation' ? ? -0.75875812 0.65137248 0.00000000 0.00000 -0.65137248 -0.75875812 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 21 'point symmetry operation' ? ? -0.61210598 0.79077574 0.00000000 0.00000 -0.79077574 -0.61210598 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 22 'point symmetry operation' ? ? -0.44039415 0.89780454 0.00000000 0.00000 -0.89780454 -0.44039415 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 23 'point symmetry operation' ? ? -0.25065253 0.96807712 0.00000000 0.00000 -0.96807712 -0.25065253 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 24 'point symmetry operation' ? ? -0.05064917 0.99871651 0.00000000 0.00000 -0.99871651 -0.05064917 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 25 'point symmetry operation' ? ? 0.15142778 0.98846832 0.00000000 0.00000 -0.98846832 0.15142778 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 26 'point symmetry operation' ? ? 0.34730525 0.93775213 0.00000000 0.00000 -0.93775213 0.34730525 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 27 'point symmetry operation' ? ? 0.52896401 0.84864426 0.00000000 0.00000 -0.84864426 0.52896401 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 28 'point symmetry operation' ? ? 0.68896692 0.72479279 0.00000000 0.00000 -0.72479279 0.68896692 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 29 'point symmetry operation' ? ? 0.82076344 0.57126822 0.00000000 0.00000 -0.57126822 0.82076344 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 30 'point symmetry operation' ? ? 0.91895781 0.39435586 0.00000000 0.00000 -0.39435586 0.91895781 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 31 'point symmetry operation' ? ? 0.97952994 0.20129852 0.00000000 0.00000 -0.20129852 0.97952994 0.00000000 0.00000 0.00000000 0.00000000 1.00000000 0.00000 # _pdbx_point_symmetry.entry_id 2BK2 _pdbx_point_symmetry.Schoenflies_symbol C _pdbx_point_symmetry.circular_symmetry 31 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2005-05-04 2 'Structure model' 1 1 2013-01-16 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Version format compliance' # _em_3d_fitting.id 1 _em_3d_fitting.entry_id 2BK2 _em_3d_fitting.ref_protocol 'RIGID BODY FIT' _em_3d_fitting.ref_space ? _em_3d_fitting.overall_b_value ? _em_3d_fitting.target_criteria ? _em_3d_fitting.details ;METHOD--THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998, CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1106). THE ALPHA CARBON TRACE OF PERFRINGOLYSIN 0 WAS MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE POSITION OF ONE SUBUNIT. THE BEST FIT WAS OBTAINED BY SEPARATING THE MONOMER INTO TWO RIGID BODIES- DOMAINS 1-3 (36-390) AND DOMAIN 4 (391-500). THE COMPLETE OLIGOMER (31-MER) WAS GENERATED AND CHECKED FOR CLOSE CONTACTS BOTH BY EYE AND USING THE CCP4 PROGRAM CONTACT. ; _em_3d_fitting.method ? # _em_3d_fitting_list.3d_fitting_id 1 _em_3d_fitting_list.id 1 _em_3d_fitting_list.pdb_entry_id 1PFO _em_3d_fitting_list.pdb_chain_id ? _em_3d_fitting_list.details ? # _em_3d_reconstruction.entry_id 2BK2 _em_3d_reconstruction.id 1 _em_3d_reconstruction.symmetry_type POINT _em_3d_reconstruction.num_particles 223 _em_3d_reconstruction.image_processing_id 1 _em_3d_reconstruction.method ? _em_3d_reconstruction.nominal_pixel_size 3.5 _em_3d_reconstruction.actual_pixel_size ? _em_3d_reconstruction.resolution 28.00 _em_3d_reconstruction.magnification_calibration ? _em_3d_reconstruction.details 'RESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. THE 31-MER CAN BE GENERATED BY APPLYING 31-FOLD ROTATIONAL SYMMETRY' _em_3d_reconstruction.num_class_averages ? _em_3d_reconstruction.resolution_method ? _em_3d_reconstruction.algorithm ? # _em_buffer.id 1 _em_buffer.pH 6.95 _em_buffer.specimen_id 1 _em_buffer.name '8 MM NA2HP04, 1.5MM KH2PO4, 2.5 MM KCL, 0.25 MM NACL' _em_buffer.details '8 MM NA2HP04, 1.5MM KH2PO4, 2.5 MM KCL, 0.25 MM NACL' # _em_entity_assembly.id 1 _em_entity_assembly.name PNEUMOLYSIN _em_entity_assembly.type COMPLEX _em_entity_assembly.parent_id 0 _em_entity_assembly.synonym ? _em_entity_assembly.details 'THE SAMPLE CONSISTS OF PNEUMOLYSIN IN A MEMBRANE-INSERTED PORE STATE' _em_entity_assembly.oligomeric_details ? # _em_image_scans.entry_id 2BK2 _em_image_scans.id 1 _em_image_scans.image_recording_id 1 _em_image_scans.number_digital_images 135 _em_image_scans.citation_id ? _em_image_scans.od_range ? _em_image_scans.quant_bit_size ? _em_image_scans.sampling_size ? _em_image_scans.scanner_model ? _em_image_scans.details ? # _em_imaging.entry_id 2BK2 _em_imaging.id 1 _em_imaging.microscope_model 'FEI TECNAI F20' _em_imaging.illumination_mode 'FLOOD BEAM' _em_imaging.electron_source 'FIELD EMISSION GUN' _em_imaging.specimen_id 1 _em_imaging.date ? _em_imaging.temperature 100 _em_imaging.nominal_defocus_min 1100 _em_imaging.nominal_defocus_max 3200 _em_imaging.tilt_angle_min 0 _em_imaging.tilt_angle_max 0 _em_imaging.nominal_cs 2 _em_imaging.mode 'BRIGHT FIELD' _em_imaging.nominal_magnification 42000 _em_imaging.calibrated_magnification ? _em_imaging.accelerating_voltage 200 _em_imaging.details 'SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.' _em_imaging.specimen_holder_type . _em_imaging.specimen_holder_model . _em_imaging.citation_id ? _em_imaging.astigmatism ? _em_imaging.detector_distance ? _em_imaging.electron_beam_tilt_params ? _em_imaging.recording_temperature_maximum ? _em_imaging.recording_temperature_minimum ? # _em_sample_support.id 1 _em_sample_support.specimen_id 1 _em_sample_support.details 'HOLEY CARBON' _em_sample_support.method ? _em_sample_support.film_material ? _em_sample_support.grid_material ? _em_sample_support.grid_mesh_size ? _em_sample_support.grid_type ? # _em_vitrification.entry_id 2BK2 _em_vitrification.id 1 _em_vitrification.instrument 'HOMEMADE PLUNGER' _em_vitrification.cryogen_name ETHANE _em_vitrification.specimen_id 1 _em_vitrification.details 'PLUNGED INTO ETHANE' _em_vitrification.citation_id ? _em_vitrification.humidity ? _em_vitrification.method ? _em_vitrification.temp ? _em_vitrification.time_resolved_state ? # _em_experiment.entry_id 2BK2 _em_experiment.id 1 _em_experiment.aggregation_state PARTICLE _em_experiment.entity_assembly_id 1 _em_experiment.reconstruction_method 'SINGLE PARTICLE' # _em_single_particle_entity.entry_id 2BK2 _em_single_particle_entity.id 1 _em_single_particle_entity.point_symmetry C31 _em_single_particle_entity.image_processing_id 1 # _em_ctf_correction.id 1 _em_ctf_correction.details 'PHASE FLIPPING' _em_ctf_correction.type ? # _em_image_processing.id 1 _em_image_processing.image_recording_id 1 _em_image_processing.details ? # _em_image_recording.details ? _em_image_recording.id 1 _em_image_recording.avg_electron_dose_per_image 20 _em_image_recording.film_or_detector_model 'KODAK SO-163 FILM' _em_image_recording.imaging_id 1 _em_image_recording.detector_mode ? _em_image_recording.average_exposure_time ? _em_image_recording.num_diffraction_images ? _em_image_recording.num_grids_imaged ? _em_image_recording.num_real_images ? # _em_specimen.experiment_id 1 _em_specimen.id 1 _em_specimen.concentration 0.05 _em_specimen.vitrification_applied YES _em_specimen.staining_applied NO _em_specimen.embedding_applied NO _em_specimen.shadowing_applied NO _em_specimen.details ? # _pdbx_coordinate_model.asym_id A _pdbx_coordinate_model.type 'CA ATOMS ONLY' #