0.014971 0.000000 0.000000 0.000000 0.014217 0.000000 0.000000 0.000000 0.009606 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 66.796 70.337 104.100 C2 H3 O2 -1 59.044 ACETATE ION non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C3 H8 O3 92.094 GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C6 H14 O2 118.174 (4R)-2-METHYLPENTANE-2,4-DIOL non-polymer C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking To be published 0353 Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution 10.2210/pdb3kog/pdb pdb_00003kog 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 100 1 Flat mirror (vertical focusing) CCD 2009-06-10 MARMOSAIC 325 mm CCD Single crystal Si(111) bent monochromator (horizontal focusing) MAD M x-ray 1 0.85503 1.0 0.97926 1.0 0.97845 1.0 BL11-1 SSRL 0.85503,0.97926,0.97845 SYNCHROTRON SSRL BEAMLINE BL11-1 27777.172 Putative pore-forming toxin 1 man polymer 59.044 ACETATE ION 3 syn non-polymer 92.094 GLYCEROL 2 syn non-polymer 118.174 (4R)-2-METHYLPENTANE-2,4-DIOL 2 syn non-polymer 18.015 water 169 nat water no yes GSCEKENIGIEVTPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKG(MSE)TGSASVT IPALKAGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNII DAYNKGVREDKVTLNDVQVLAHSRFSVFVDY(MSE)KTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGH APSHGHGHGHGDDSNAGGGIIIAD GSCEKENIGIEVTPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKGMTGSASVTIPAL KAGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNIIDAYN KGVREDKVTLNDVQVLAHSRFSVFVDYMKTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGHAPSHGHGH GHGDDSNAGGGIIIAD A 393242 polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n ATCC 8482 / DSM 1447 / NCTC 11154 sample BVU_4064 435590 Bacteroides vulgatus ATCC 8482 562 Escherichia Coli HK100 Plasmid SpeedET 1 2.20 44.11 VAPOR DIFFUSION, SITTING DROP 4.43 31.6000% 2-methyl-2,4-pentanediol, 0.2000M sodium chloride, 0.1M sodium acetate pH 4.43, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K 293 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software pdbx_struct_special_symmetry software struct_conn database_2 struct_ref_seq_dif struct_site repository Initial release Advisory Version format compliance Refinement description Data collection Derived calculations Refinement description Database references Derived calculations 1 0 2009-12-01 1 1 2011-07-13 1 2 2017-11-01 1 3 2019-07-17 1 4 2023-02-01 _software.classification _software.name _software.classification _software.contact_author _software.contact_author_email _software.language _software.location _software.name _software.type _software.version _struct_conn.pdbx_leaving_atom_flag _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y RCSB Y RCSB 2009-11-13 REL REL ACT ACETATE ION GOL GLYCEROL MRD (4R)-2-METHYLPENTANE-2,4-DIOL HOH water SEQUENCE THIS CONSTRUCT (28-282) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ACT 1 2 ACT ACT 1 A ACT 2 2 ACT ACT 2 A ACT 3 2 ACT ACT 3 A GOL 4 3 GOL GOL 4 A GOL 5 3 GOL GOL 5 A MRD 6 4 MRD MRD 6 A MRD 7 4 MRD MRD 7 A HOH 8 5 HOH HOH 8 A HOH 9 5 HOH HOH 9 A HOH 10 5 HOH HOH 10 A HOH 11 5 HOH HOH 11 A HOH 12 5 HOH HOH 12 A HOH 13 5 HOH HOH 13 A HOH 14 5 HOH HOH 14 A HOH 15 5 HOH HOH 15 A HOH 16 5 HOH HOH 16 A HOH 17 5 HOH HOH 17 A HOH 18 5 HOH HOH 18 A HOH 19 5 HOH HOH 19 A HOH 20 5 HOH HOH 20 A HOH 21 5 HOH HOH 21 A HOH 22 5 HOH HOH 22 A HOH 23 5 HOH HOH 23 A HOH 24 5 HOH HOH 24 A HOH 25 5 HOH HOH 25 A HOH 26 5 HOH HOH 26 A HOH 27 5 HOH HOH 283 A HOH 28 5 HOH HOH 284 A HOH 29 5 HOH HOH 285 A HOH 30 5 HOH HOH 286 A HOH 31 5 HOH HOH 287 A HOH 32 5 HOH HOH 288 A HOH 33 5 HOH HOH 289 A HOH 34 5 HOH HOH 290 A HOH 35 5 HOH HOH 291 A HOH 36 5 HOH HOH 292 A HOH 37 5 HOH HOH 293 A HOH 38 5 HOH HOH 294 A HOH 39 5 HOH HOH 295 A HOH 40 5 HOH HOH 296 A HOH 41 5 HOH HOH 297 A HOH 42 5 HOH HOH 298 A HOH 43 5 HOH HOH 299 A HOH 44 5 HOH HOH 300 A HOH 45 5 HOH HOH 301 A HOH 46 5 HOH HOH 302 A HOH 47 5 HOH HOH 303 A HOH 48 5 HOH HOH 304 A HOH 49 5 HOH HOH 305 A HOH 50 5 HOH HOH 306 A HOH 51 5 HOH HOH 307 A HOH 52 5 HOH HOH 308 A HOH 53 5 HOH HOH 309 A HOH 54 5 HOH HOH 310 A HOH 55 5 HOH HOH 311 A HOH 56 5 HOH HOH 312 A HOH 57 5 HOH HOH 313 A HOH 58 5 HOH HOH 314 A HOH 59 5 HOH HOH 315 A HOH 60 5 HOH HOH 316 A HOH 61 5 HOH HOH 317 A HOH 62 5 HOH HOH 318 A HOH 63 5 HOH HOH 319 A HOH 64 5 HOH HOH 320 A HOH 65 5 HOH HOH 321 A HOH 66 5 HOH HOH 322 A HOH 67 5 HOH HOH 323 A HOH 68 5 HOH HOH 324 A HOH 69 5 HOH HOH 325 A HOH 70 5 HOH HOH 326 A HOH 71 5 HOH HOH 327 A HOH 72 5 HOH HOH 328 A HOH 73 5 HOH HOH 329 A HOH 74 5 HOH HOH 330 A HOH 75 5 HOH HOH 331 A HOH 76 5 HOH HOH 332 A HOH 77 5 HOH HOH 333 A HOH 78 5 HOH HOH 334 A HOH 79 5 HOH HOH 335 A HOH 80 5 HOH HOH 336 A HOH 81 5 HOH HOH 337 A HOH 82 5 HOH HOH 338 A HOH 83 5 HOH HOH 339 A HOH 84 5 HOH HOH 340 A HOH 85 5 HOH HOH 341 A HOH 86 5 HOH HOH 342 A HOH 87 5 HOH HOH 343 A HOH 88 5 HOH HOH 344 A HOH 89 5 HOH HOH 345 A HOH 90 5 HOH HOH 346 A HOH 91 5 HOH HOH 347 A HOH 92 5 HOH HOH 348 A HOH 93 5 HOH HOH 349 A HOH 94 5 HOH HOH 350 A HOH 95 5 HOH HOH 351 A HOH 96 5 HOH HOH 352 A HOH 97 5 HOH HOH 353 A HOH 98 5 HOH HOH 354 A HOH 99 5 HOH HOH 355 A HOH 100 5 HOH HOH 356 A HOH 101 5 HOH HOH 357 A HOH 102 5 HOH HOH 358 A HOH 103 5 HOH HOH 359 A HOH 104 5 HOH HOH 360 A HOH 105 5 HOH HOH 361 A HOH 106 5 HOH HOH 362 A HOH 107 5 HOH HOH 363 A HOH 108 5 HOH HOH 364 A HOH 109 5 HOH HOH 365 A HOH 110 5 HOH HOH 366 A HOH 111 5 HOH HOH 367 A HOH 112 5 HOH HOH 368 A HOH 113 5 HOH HOH 369 A HOH 114 5 HOH HOH 370 A HOH 115 5 HOH HOH 371 A HOH 116 5 HOH HOH 372 A HOH 117 5 HOH HOH 373 A HOH 118 5 HOH HOH 374 A HOH 119 5 HOH HOH 375 A HOH 120 5 HOH HOH 376 A HOH 121 5 HOH HOH 377 A HOH 122 5 HOH HOH 378 A HOH 123 5 HOH HOH 379 A HOH 124 5 HOH HOH 380 A HOH 125 5 HOH HOH 381 A HOH 126 5 HOH HOH 382 A HOH 127 5 HOH HOH 383 A HOH 128 5 HOH HOH 384 A HOH 129 5 HOH HOH 385 A HOH 130 5 HOH HOH 386 A HOH 131 5 HOH HOH 387 A HOH 132 5 HOH HOH 388 A HOH 133 5 HOH HOH 389 A HOH 134 5 HOH HOH 390 A HOH 135 5 HOH HOH 391 A HOH 136 5 HOH HOH 392 A HOH 137 5 HOH HOH 393 A HOH 138 5 HOH HOH 394 A HOH 139 5 HOH HOH 395 A HOH 140 5 HOH HOH 396 A HOH 141 5 HOH HOH 397 A HOH 142 5 HOH HOH 398 A HOH 143 5 HOH HOH 399 A HOH 144 5 HOH HOH 400 A HOH 145 5 HOH HOH 401 A HOH 146 5 HOH HOH 402 A HOH 147 5 HOH HOH 403 A HOH 148 5 HOH HOH 404 A HOH 149 5 HOH HOH 405 A HOH 150 5 HOH HOH 406 A HOH 151 5 HOH HOH 407 A HOH 152 5 HOH HOH 408 A HOH 153 5 HOH HOH 409 A HOH 154 5 HOH HOH 410 A HOH 155 5 HOH HOH 411 A HOH 156 5 HOH HOH 412 A HOH 157 5 HOH HOH 413 A HOH 158 5 HOH HOH 414 A HOH 159 5 HOH HOH 415 A HOH 160 5 HOH HOH 416 A HOH 161 5 HOH HOH 417 A HOH 162 5 HOH HOH 418 A HOH 163 5 HOH HOH 419 A HOH 164 5 HOH HOH 420 A HOH 165 5 HOH HOH 421 A HOH 166 5 HOH HOH 422 A HOH 167 5 HOH HOH 423 A HOH 168 5 HOH HOH 424 A HOH 169 5 HOH HOH 425 A HOH 170 5 HOH HOH 426 A HOH 171 5 HOH HOH 427 A HOH 172 5 HOH HOH 428 A HOH 173 5 HOH HOH 429 A HOH 174 5 HOH HOH 430 A HOH 175 5 HOH HOH 431 A HOH 176 5 HOH HOH 432 A n 1 0 A n 2 28 A n 3 29 A n 4 30 A n 5 31 A n 6 32 A n 7 33 A n 8 34 A n 9 35 A n 10 36 A n 11 37 A n 12 38 A THR 39 n 13 THR 39 A PRO 40 n 14 PRO 40 A VAL 41 n 15 VAL 41 A ASN 42 n 16 ASN 42 A ALA 43 n 17 ALA 43 A LYS 44 n 18 LYS 44 A PHE 45 n 19 PHE 45 A ILE 46 n 20 ILE 46 A ILE 47 n 21 ILE 47 A THR 48 n 22 THR 48 A PRO 49 n 23 PRO 49 A VAL 50 n 24 VAL 50 A VAL 51 n 25 VAL 51 A ILE 52 n 26 ILE 52 A ASP 53 n 27 ASP 53 A ALA 54 n 28 ALA 54 A THR 55 n 29 THR 55 A THR 56 n 30 THR 56 A GLY 57 n 31 GLY 57 A THR 58 n 32 THR 58 A ASP 59 n 33 ASP 59 A VAL 60 n 34 VAL 60 A THR 61 n 35 THR 61 A GLN 62 n 36 GLN 62 A SER 63 n 37 SER 63 A ALA 64 n 38 ALA 64 A GLU 65 n 39 GLU 65 A ILE 66 n 40 ILE 66 A SER 67 n 41 SER 67 A PHE 68 n 42 PHE 68 A SER 69 n 43 SER 69 A LYS 70 n 44 LYS 70 A GLY 71 n 45 GLY 71 A ASN 72 n 46 ASN 72 A GLY 73 n 47 GLY 73 A THR 74 n 48 THR 74 A TYR 75 n 49 TYR 75 A GLU 76 n 50 GLU 76 A GLY 77 n 51 GLY 77 A THR 78 n 52 THR 78 A PRO 79 n 53 PRO 79 A GLU 80 n 54 GLU 80 A LEU 81 n 55 LEU 81 A ALA 82 n 56 ALA 82 A SER 83 n 57 SER 83 A GLU 84 n 58 GLU 84 A SER 85 n 59 SER 85 A ILE 86 n 60 ILE 86 A ASN 87 n 61 ASN 87 A ILE 88 n 62 ILE 88 A ASN 89 n 63 ASN 89 A ALA 90 n 64 ALA 90 A LYS 91 n 65 LYS 91 A TYR 92 n 66 TYR 92 A LYS 93 n 67 LYS 93 A GLY 94 n 68 GLY 94 A MSE 95 n 69 MSE 95 A THR 96 n 70 THR 96 A GLY 97 n 71 GLY 97 A SER 98 n 72 SER 98 A ALA 99 n 73 ALA 99 A SER 100 n 74 SER 100 A VAL 101 n 75 VAL 101 A THR 102 n 76 THR 102 A ILE 103 n 77 ILE 103 A PRO 104 n 78 PRO 104 A ALA 105 n 79 ALA 105 A LEU 106 n 80 LEU 106 A LYS 107 n 81 LYS 107 A ALA 108 n 82 ALA 108 A GLY 109 n 83 GLY 109 A GLN 110 n 84 GLN 110 A PHE 111 n 85 PHE 111 A GLY 112 n 86 GLY 112 A ALA 113 n 87 ALA 113 A LYS 114 n 88 LYS 114 A GLU 115 n 89 GLU 115 A VAL 116 n 90 VAL 116 A THR 117 n 91 THR 117 A ILE 118 n 92 ILE 118 A ILE 119 n 93 ILE 119 A LEU 120 n 94 LEU 120 A SER 121 n 95 SER 121 A GLU 122 n 96 GLU 122 A ASN 123 n 97 ASN 123 A PHE 124 n 98 PHE 124 A PHE 125 n 99 PHE 125 A ALA 126 n 100 ALA 126 A GLN 127 n 101 GLN 127 A GLU 128 n 102 GLU 128 A GLU 129 n 103 GLU 129 A SER 130 n 104 SER 130 A SER 131 n 105 SER 131 A ASN 132 n 106 ASN 132 A SER 133 n 107 SER 133 A GLN 134 n 108 GLN 134 A ILE 135 n 109 ILE 135 A GLU 136 n 110 GLU 136 A THR 137 n 111 THR 137 A THR 138 n 112 THR 138 A LYS 139 n 113 LYS 139 A HIS 140 n 114 HIS 140 A SER 141 n 115 SER 141 A GLY 142 n 116 GLY 142 A PHE 143 n 117 PHE 143 A LYS 144 n 118 LYS 144 A ASN 145 n 119 ASN 145 A ASN 146 n 120 ASN 146 A THR 147 n 121 THR 147 A SER 148 n 122 SER 148 A ASP 149 n 123 ASP 149 A TYR 150 n 124 TYR 150 A TRP 151 n 125 TRP 151 A TYR 152 n 126 TYR 152 A TYR 153 n 127 TYR 153 A ILE 154 n 128 ILE 154 A THR 155 n 129 THR 155 A VAL 156 n 130 VAL 156 A THR 157 n 131 THR 157 A TYR 158 n 132 TYR 158 A THR 159 n 133 THR 159 A LYS 160 n 134 LYS 160 A LYS 161 n 135 LYS 161 A GLU 162 n 136 GLU 162 A GLY 163 n 137 GLY 163 A SER 164 n 138 SER 164 A GLU 165 n 139 GLU 165 A VAL 166 n 140 VAL 166 A ILE 167 n 141 ILE 167 A LYS 168 n 142 LYS 168 A ASN 169 n 143 ASN 169 A ASP 170 n 144 ASP 170 A TYR 171 n 145 TYR 171 A GLU 172 n 146 GLU 172 A GLY 173 n 147 GLY 173 A ASP 174 n 148 ASP 174 A ASP 175 n 149 ASP 175 A SER 176 n 150 SER 176 A GLU 177 n 151 GLU 177 A ILE 178 n 152 ILE 178 A LYS 179 n 153 LYS 179 A ASN 180 n 154 ASN 180 A ILE 181 n 155 ILE 181 A ILE 182 n 156 ILE 182 A ASP 183 n 157 ASP 183 A ALA 184 n 158 ALA 184 A TYR 185 n 159 TYR 185 A ASN 186 n 160 ASN 186 A LYS 187 n 161 LYS 187 A GLY 188 n 162 GLY 188 A VAL 189 n 163 VAL 189 A ARG 190 n 164 ARG 190 A GLU 191 n 165 GLU 191 A ASP 192 n 166 ASP 192 A LYS 193 n 167 LYS 193 A VAL 194 n 168 VAL 194 A THR 195 n 169 THR 195 A LEU 196 n 170 LEU 196 A ASN 197 n 171 ASN 197 A ASP 198 n 172 ASP 198 A VAL 199 n 173 VAL 199 A GLN 200 n 174 GLN 200 A VAL 201 n 175 VAL 201 A LEU 202 n 176 LEU 202 A ALA 203 n 177 ALA 203 A HIS 204 n 178 HIS 204 A SER 205 n 179 SER 205 A ARG 206 n 180 ARG 206 A PHE 207 n 181 PHE 207 A SER 208 n 182 SER 208 A VAL 209 n 183 VAL 209 A PHE 210 n 184 PHE 210 A VAL 211 n 185 VAL 211 A ASP 212 n 186 ASP 212 A TYR 213 n 187 TYR 213 A MSE 214 n 188 MSE 214 A LYS 215 n 189 LYS 215 A THR 216 n 190 THR 216 A THR 217 n 191 THR 217 A SER 218 n 192 SER 218 A VAL 219 n 193 VAL 219 A TYR 220 n 194 TYR 220 A GLN 221 n 195 GLN 221 A ILE 222 n 196 ILE 222 A ILE 223 n 197 ILE 223 A GLU 224 n 198 GLU 224 A LYS 225 n 199 LYS 225 A SER 226 n 200 SER 226 A PRO 227 n 201 PRO 227 A n 202 228 A n 203 229 A ASP 230 n 204 ASP 230 A GLY 231 n 205 GLY 231 A ASN 232 n 206 ASN 232 A PRO 233 n 207 PRO 233 A VAL 234 n 208 VAL 234 A ALA 235 n 209 ALA 235 A SER 236 n 210 SER 236 A PHE 237 n 211 PHE 237 A THR 238 n 212 THR 238 A VAL 239 n 213 VAL 239 A ASP 240 n 214 ASP 240 A SER 241 n 215 SER 241 A TYR 242 n 216 TYR 242 A ASN 243 n 217 ASN 243 A THR 244 n 218 THR 244 A ILE 245 n 219 ILE 245 A VAL 246 n 220 VAL 246 A SER 247 n 221 SER 247 A PRO 248 n 222 PRO 248 A LYS 249 n 223 LYS 249 A ASN 250 n 224 ASN 250 A GLU 251 n 225 GLU 251 A GLN 252 n 226 GLN 252 A ILE 253 n 227 ILE 253 A PRO 254 n 228 PRO 254 A GLY 255 n 229 GLY 255 A HIS 256 n 230 HIS 256 A GLY 257 n 231 GLY 257 A HIS 258 n 232 HIS 258 A ALA 259 n 233 ALA 259 A PRO 260 n 234 PRO 260 A SER 261 n 235 SER 261 A HIS 262 n 236 HIS 262 A GLY 263 n 237 GLY 263 A HIS 264 n 238 HIS 264 A GLY 265 n 239 GLY 265 A HIS 266 n 240 HIS 266 A n 241 267 A n 242 268 A n 243 269 A n 244 270 A n 245 271 A n 246 272 A n 247 273 A n 248 274 A n 249 275 A n 250 276 A n 251 277 A n 252 278 A n 253 279 A n 254 280 A n 255 281 A n 256 282 A 1.4965 -0.3392 0.2804 1.2485 0.3460 0.7718 -0.0912 -0.0271 0.0376 -0.0529 0.1747 -0.1794 -0.0804 -0.0569 -0.0835 0.0384 -0.0094 0.0137 0.0656 0.0004 0.0528 refined 29.1910 26.4290 48.5930 X-RAY DIFFRACTION 3.5387 2.3669 3.5712 3.3044 3.4333 4.7673 -0.0092 0.4123 -0.1249 -0.0845 0.2816 -0.2361 -0.1165 0.3624 -0.2725 0.0635 -0.0047 0.0352 0.1039 0.0158 0.0501 refined 26.7700 29.9400 38.4470 X-RAY DIFFRACTION A 39 A 145 X-RAY DIFFRACTION 1 A 146 A 266 X-RAY DIFFRACTION 2 author_defined_assembly 1 monomeric A MSE 95 SELENOMETHIONINE A MSE 69 MET A MSE 214 SELENOMETHIONINE A MSE 188 MET 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O TYR 75 A O TYR 49 A N PHE 45 A N PHE 19 A N ILE 52 A N ILE 26 A O LEU 120 A O LEU 94 A N PHE 111 A N PHE 85 A O VAL 246 A O VAL 220 A O SER 241 A O SER 215 A N THR 216 A N THR 190 A O SER 205 A O SER 179 A N ASN 146 A N ASN 120 A N GLN 127 A N GLN 101 A O GLN 221 A O GLN 195 A N THR 216 A N THR 190 A O SER 241 A O SER 215 A O TYR 242 A O TYR 216 A N GLY 163 A N GLY 137 A N GLU 162 A N GLU 136 A O ARG 190 A O ARG 164 A N SER 67 A N SER 41 A O ASN 89 A O ASN 63 A N ILE 88 A N ILE 62 A O ALA 99 A O ALA 73 1 A MRD 7 H MRD 1 A CE LYS 91 A CE LYS 65 1 Y 1 A NZ LYS 91 A NZ LYS 65 1 Y 1 A CE LYS 107 A CE LYS 81 1 Y 1 A NZ LYS 107 A NZ LYS 81 1 Y 1 A CE LYS 144 A CE LYS 118 1 Y 1 A NZ LYS 144 A NZ LYS 118 1 Y 1 A NZ LYS 160 A NZ LYS 134 1 Y 1 A NZ LYS 193 A NZ LYS 167 1 Y 1 A CG ASN 197 A CG ASN 171 1 Y 1 A OD1 ASN 197 A OD1 ASN 171 1 Y 1 A ND2 ASN 197 A ND2 ASN 171 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A SER 28 A SER 2 1 Y 1 A CYS 29 A CYS 3 1 Y 1 A GLU 30 A GLU 4 1 Y 1 A LYS 31 A LYS 5 1 Y 1 A GLU 32 A GLU 6 1 Y 1 A ASN 33 A ASN 7 1 Y 1 A ILE 34 A ILE 8 1 Y 1 A GLY 35 A GLY 9 1 Y 1 A ILE 36 A ILE 10 1 Y 1 A GLU 37 A GLU 11 1 Y 1 A VAL 38 A VAL 12 1 Y 1 A LYS 228 A LYS 202 1 Y 1 A ARG 229 A ARG 203 1 Y 1 A GLY 267 A GLY 241 1 Y 1 A HIS 268 A HIS 242 1 Y 1 A GLY 269 A GLY 243 1 Y 1 A ASP 270 A ASP 244 1 Y 1 A ASP 271 A ASP 245 1 Y 1 A SER 272 A SER 246 1 Y 1 A ASN 273 A ASN 247 1 Y 1 A ALA 274 A ALA 248 1 Y 1 A GLY 275 A GLY 249 1 Y 1 A GLY 276 A GLY 250 1 Y 1 A GLY 277 A GLY 251 1 Y 1 A ILE 278 A ILE 252 1 Y 1 A ILE 279 A ILE 253 1 Y 1 A ILE 280 A ILE 254 1 Y 1 A ALA 281 A ALA 255 1 Y 1 A ASP 282 A ASP 256 1 Y 1 A A OE1 O GLU HOH 65 307 2.14 B 1 A A OD2 OE2 ASP GLU 170 172 2.13 A 1_555 6_665 66.51 18.402 4.15 -0.250 0.000 0.000 -0.070 0.000 0.310 0.956 0.945 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE (ACT), GLYCEROL (GOL), AND (4R)-2-METHYL-2,4-PENTANEDIOL (MRD) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER. 0.214 0.182 0.184 1.850 29.814 1095 21310 5.100 99.990 1.00 0.25 6.503 0.088 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MAD 0.142 0.129 0.800 0.800 1.400 MAXIMUM LIKELIHOOD WITH PHASES MASK 1.850 29.814 169 1938 40 0 1729 0.018 0.022 1944 0.002 0.020 1260 1.621 1.953 2673 0.930 3.000 3143 6.642 5.000 272 39.549 26.264 91 14.076 15.000 325 17.383 15.000 3 0.102 0.200 303 0.007 0.020 2222 0.001 0.020 360 0.959 1.500 1204 0.277 1.500 484 1.697 2.000 1981 2.690 3.000 740 4.300 4.500 669 0.304 0.271 1.898 73 1468 1541 20 100.000 21.528 1.85 29.814 3KOG 21313 0.091 0.091 1 10.200 4.100 100.000 0.726 1.85 1.90 1.0 6377 1549 0.726 1 4.10 100.00 0.565 1.90 1.95 1.0 6196 1507 0.565 1 4.10 100.00 0.439 1.95 2.01 1.7 6068 1475 0.439 1 4.10 100.00 0.340 2.01 2.07 2.1 5914 1437 0.340 1 4.10 100.00 0.294 2.07 2.14 2.5 5672 1378 0.294 1 4.10 100.00 0.262 2.14 2.21 2.8 5591 1355 0.262 1 4.10 100.00 0.220 2.21 2.29 3.3 5376 1309 0.220 1 4.10 100.00 0.189 2.29 2.39 3.9 5139 1246 0.189 1 4.10 100.00 0.167 2.39 2.49 4.4 4928 1201 0.167 1 4.10 100.00 0.142 2.49 2.62 5.0 4762 1163 0.142 1 4.10 100.00 0.115 2.62 2.76 6.2 4495 1098 0.115 1 4.10 100.00 0.097 2.76 2.93 7.1 4235 1035 0.097 1 4.10 100.00 0.081 2.93 3.13 8.1 4029 987 0.081 1 4.10 100.00 0.067 3.13 3.38 9.5 3777 928 0.067 1 4.10 100.00 0.053 3.38 3.70 11.8 3482 858 0.053 1 4.10 100.00 0.043 3.70 4.14 13.8 3093 763 0.043 1 4.10 100.00 0.043 4.14 4.78 13.7 2762 691 0.043 1 4.00 100.00 0.046 4.78 5.85 12.9 2342 591 0.046 1 4.00 100.00 0.043 5.85 8.27 14.2 1787 467 0.043 1 3.80 100.00 0.039 8.27 29.82 15.3 963 275 0.039 1 3.50 98.00 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0053 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package phasing Tom Terwilliger terwilliger@LANL.gov http://www.solve.lanl.gov/ SOLVE program model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data scaling Phil R. Evans pre@mrc-lmb.cam.ac.uk 5/04/2004 Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other 3.2.5 data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.006 data reduction MOSFLM Crystal structure of Putative pore-forming toxin (YP_001301288.1) from Bacteroides vulgatus ATCC 8482 at 1.85 A resolution 1 N N 2 N N 2 N N 2 N N 3 N N 3 N N 4 N N 4 N N 5 N N A VAL 60 A VAL 34 HELX_P A ALA 64 A ALA 38 5 1 5 A ASP 175 A ASP 149 HELX_P A TYR 185 A TYR 159 1 2 11 covale 1.323 both A MSE 95 A C MSE 69 1_555 A THR 96 A N THR 70 1_555 covale 1.329 both A MSE 214 A C MSE 188 1_555 A LYS 215 A N LYS 189 1_555 MEMBRANE PROTEIN Putative pore-forming toxin, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, MEMBRANE PROTEIN A THR 78 A THR 52 1 A PRO 79 A PRO 53 9.00 A6L7K2_BACV8 UNP 1 28 A6L7K2 SCEKENIGIEVTPVNAKFIITPVVIDATTGTDVTQSAEISFSKGNGTYEGTPELASESININAKYKGMTGSASVTIPALK AGQFGAKEVTIILSENFFAQEESSNSQIETTKHSGFKNNTSDYWYYITVTYTKKEGSEVIKNDYEGDDSEIKNIIDAYNK GVREDKVTLNDVQVLAHSRFSVFVDYMKTTSVYQIIEKSPKRDGNPVASFTVDSYNTIVSPKNEQIPGHGHAPSHGHGHG HGDDSNAGGGIIIAD 28 282 3KOG 28 282 A6L7K2 A 1 2 256 1 expression tag GLY 0 3KOG A A6L7K2 UNP 1 6 5 3 anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A THR 74 A THR 48 A GLU 76 A GLU 50 A LYS 44 A LYS 18 A ASP 53 A ASP 27 A PHE 111 A PHE 85 A LEU 120 A LEU 94 A PRO 233 A PRO 207 A GLU 251 A GLU 225 A SER 205 A SER 179 A GLU 224 A GLU 198 A LYS 144 A LYS 118 A ASN 146 A ASN 120 A PHE 124 A PHE 98 A HIS 140 A HIS 114 A SER 205 A SER 179 A GLU 224 A GLU 198 A PRO 233 A PRO 207 A GLU 251 A GLU 225 A TYR 152 A TYR 126 A ASN 169 A ASN 143 A GLY 188 A GLY 162 A VAL 201 A VAL 175 A GLU 65 A GLU 39 A PHE 68 A PHE 42 A GLU 84 A GLU 58 A TYR 92 A TYR 66 A MSE 95 A MSE 69 A ILE 103 A ILE 77 BINDING SITE FOR RESIDUE ACT A 1 A ACT 1 Software 2 BINDING SITE FOR RESIDUE ACT A 2 A ACT 2 Software 1 BINDING SITE FOR RESIDUE GOL A 4 A GOL 4 Software 8 BINDING SITE FOR RESIDUE GOL A 5 A GOL 5 Software 7 BINDING SITE FOR RESIDUE MRD A 6 A MRD 6 Software 3 BINDING SITE FOR RESIDUE MRD A 7 A MRD 7 Software 5 A HOH 390 I HOH 2 1_555 A HOH 391 I HOH 2 1_555 A SER 130 A SER 104 1 1_555 A HOH 13 I HOH 8 1_555 A GLU 115 A GLU 89 8 1_555 A VAL 116 A VAL 90 8 1_555 A THR 117 A THR 91 8 1_555 A SER 164 A SER 138 8 1_555 A TYR 185 A TYR 159 8 1_555 A HOH 311 I HOH 8 1_555 A HOH 410 I HOH 8 1_555 A HOH 25 I HOH 7 1_555 A ASP 59 A ASP 33 7 1_555 A VAL 60 A VAL 34 7 1_555 A THR 61 A THR 35 7 1_555 A GLN 62 A GLN 36 7 1_555 A HOH 319 I HOH 7 6_655 A HOH 328 I HOH 7 1_555 A GLN 110 A GLN 84 3 1_555 A ASP 212 A ASP 186 3 1_555 A HOH 305 I HOH 3 1_555 A SER 83 A SER 57 5 1_555 A SER 83 A SER 57 5 7_556 A SER 85 A SER 59 5 7_556 A SER 85 A SER 59 5 1_555 A THR 102 A THR 76 5 1_555 24 I 21 21 21