0.010137 0.005852 0.000000 0.000000 0.011705 0.000000 0.000000 0.000000 0.005128 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 98.653 98.653 195.018 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 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 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 C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C8 H18 O5 194.226 TETRAETHYLENE GLYCOL non-polymer 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 a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution 10.2210/pdb4r4g/pdb pdb_00004r4g 100 1 Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) PIXEL 2014-06-26 DECTRIS PILATUS 6M single crystal Si(111) bent MAD M x-ray 1 0.97971 1.0 0.91837 1.0 0.97926 1.0 BL11-1 SSRL 0.97971,0.91837,0.97926 SYNCHROTRON SSRL BEAMLINE BL11-1 36286.562 putative lipoprotein YcdA 1 man polymer 194.226 TETRAETHYLENE GLYCOL 3 syn non-polymer 18.015 water 33 nat water no yes GEKKESETEKSSDIAQVKIKDVSYTLPSKYDKSTSDDQLVLKVNVAVKNTGKDPLNVDS(MSE)DFTLYQGDTK(MSE)S DTDPEDYSEKLQGSTINADKSVEGNLFFVVDKGKQYELNYTPESYGDKKPKSVTFKIDGKDKKILATADKLQDSAKALSA YVDVLLFGKDNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKD EAIVEATVKPVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVK(MSE)KKNDIDQWQ LD(MSE)DDYRAAELVEAFIKE GEKKESETEKSSDIAQVKIKDVSYTLPSKYDKSTSDDQLVLKVNVAVKNTGKDPLNVDSMDFTLYQGDTKMSDTDPEDYS EKLQGSTINADKSVEGNLFFVVDKGKQYELNYTPESYGDKKPKSVTFKIDGKDKKILATADKLQDSAKALSAYVDVLLFG KDNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKDEAIVEATV KPVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVKMKKNDIDQWQLDMDDYRAAELV EAFIKE A JCSG-418973 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 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 sample ycdA, BSU02780 224308 Bacillus subtilis subsp. subtilis str. 168 562 Escherichia Coli PB1 Plasmid SpeedET 1 3.77 67.42 VAPOR DIFFUSION, SITTING DROP 7.0 50.0% polyethylene glycol 200, 0.1M TRIS pH 7.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI:Biology software citation_author database_2 struct_conn struct_ref_seq_dif struct_site repository Initial release Refinement description Database references Database references Derived calculations 1 0 2014-09-17 1 1 2017-11-22 1 2 2018-01-24 1 3 2023-02-01 _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _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 2014-08-19 REL REL PG4 TETRAETHYLENE GLYCOL HOH water THE CONSTRUCT (30-354) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. PG4 401 2 PG4 PG4 401 A PG4 402 2 PG4 PG4 402 A PG4 403 2 PG4 PG4 403 A HOH 404 3 HOH HOH 501 A HOH 405 3 HOH HOH 502 A HOH 406 3 HOH HOH 503 A HOH 407 3 HOH HOH 504 A HOH 408 3 HOH HOH 505 A HOH 409 3 HOH HOH 506 A HOH 410 3 HOH HOH 507 A HOH 411 3 HOH HOH 508 A HOH 412 3 HOH HOH 509 A HOH 413 3 HOH HOH 510 A HOH 414 3 HOH HOH 511 A HOH 415 3 HOH HOH 512 A HOH 416 3 HOH HOH 513 A HOH 417 3 HOH HOH 514 A HOH 418 3 HOH HOH 515 A HOH 419 3 HOH HOH 516 A HOH 420 3 HOH HOH 517 A HOH 421 3 HOH HOH 518 A HOH 422 3 HOH HOH 519 A HOH 423 3 HOH HOH 520 A HOH 424 3 HOH HOH 521 A HOH 425 3 HOH HOH 522 A HOH 426 3 HOH HOH 523 A HOH 427 3 HOH HOH 524 A HOH 428 3 HOH HOH 525 A HOH 429 3 HOH HOH 526 A HOH 430 3 HOH HOH 527 A HOH 431 3 HOH HOH 528 A HOH 432 3 HOH HOH 529 A HOH 433 3 HOH HOH 530 A HOH 434 3 HOH HOH 531 A HOH 435 3 HOH HOH 532 A HOH 436 3 HOH HOH 533 A n 1 0 A n 2 30 A n 3 31 A n 4 32 A GLU 33 n 5 GLU 33 A SER 34 n 6 SER 34 A GLU 35 n 7 GLU 35 A THR 36 n 8 THR 36 A GLU 37 n 9 GLU 37 A LYS 38 n 10 LYS 38 A SER 39 n 11 SER 39 A SER 40 n 12 SER 40 A ASP 41 n 13 ASP 41 A ILE 42 n 14 ILE 42 A ALA 43 n 15 ALA 43 A GLN 44 n 16 GLN 44 A VAL 45 n 17 VAL 45 A LYS 46 n 18 LYS 46 A ILE 47 n 19 ILE 47 A LYS 48 n 20 LYS 48 A ASP 49 n 21 ASP 49 A VAL 50 n 22 VAL 50 A SER 51 n 23 SER 51 A TYR 52 n 24 TYR 52 A THR 53 n 25 THR 53 A LEU 54 n 26 LEU 54 A PRO 55 n 27 PRO 55 A SER 56 n 28 SER 56 A LYS 57 n 29 LYS 57 A TYR 58 n 30 TYR 58 A ASP 59 n 31 ASP 59 A LYS 60 n 32 LYS 60 A SER 61 n 33 SER 61 A THR 62 n 34 THR 62 A SER 63 n 35 SER 63 A ASP 64 n 36 ASP 64 A ASP 65 n 37 ASP 65 A GLN 66 n 38 GLN 66 A LEU 67 n 39 LEU 67 A VAL 68 n 40 VAL 68 A LEU 69 n 41 LEU 69 A LYS 70 n 42 LYS 70 A VAL 71 n 43 VAL 71 A ASN 72 n 44 ASN 72 A VAL 73 n 45 VAL 73 A ALA 74 n 46 ALA 74 A VAL 75 n 47 VAL 75 A LYS 76 n 48 LYS 76 A ASN 77 n 49 ASN 77 A THR 78 n 50 THR 78 A GLY 79 n 51 GLY 79 A LYS 80 n 52 LYS 80 A ASP 81 n 53 ASP 81 A PRO 82 n 54 PRO 82 A LEU 83 n 55 LEU 83 A ASN 84 n 56 ASN 84 A VAL 85 n 57 VAL 85 A ASP 86 n 58 ASP 86 A SER 87 n 59 SER 87 A MSE 88 n 60 MSE 88 A ASP 89 n 61 ASP 89 A PHE 90 n 62 PHE 90 A THR 91 n 63 THR 91 A LEU 92 n 64 LEU 92 A TYR 93 n 65 TYR 93 A GLN 94 n 66 GLN 94 A GLY 95 n 67 GLY 95 A ASP 96 n 68 ASP 96 A THR 97 n 69 THR 97 A LYS 98 n 70 LYS 98 A MSE 99 n 71 MSE 99 A SER 100 n 72 SER 100 A ASP 101 n 73 ASP 101 A THR 102 n 74 THR 102 A ASP 103 n 75 ASP 103 A PRO 104 n 76 PRO 104 A GLU 105 n 77 GLU 105 A ASP 106 n 78 ASP 106 A TYR 107 n 79 TYR 107 A SER 108 n 80 SER 108 A GLU 109 n 81 GLU 109 A LYS 110 n 82 LYS 110 A LEU 111 n 83 LEU 111 A GLN 112 n 84 GLN 112 A GLY 113 n 85 GLY 113 A SER 114 n 86 SER 114 A THR 115 n 87 THR 115 A ILE 116 n 88 ILE 116 A ASN 117 n 89 ASN 117 A ALA 118 n 90 ALA 118 A ASP 119 n 91 ASP 119 A LYS 120 n 92 LYS 120 A SER 121 n 93 SER 121 A VAL 122 n 94 VAL 122 A GLU 123 n 95 GLU 123 A GLY 124 n 96 GLY 124 A ASN 125 n 97 ASN 125 A LEU 126 n 98 LEU 126 A PHE 127 n 99 PHE 127 A PHE 128 n 100 PHE 128 A VAL 129 n 101 VAL 129 A VAL 130 n 102 VAL 130 A ASP 131 n 103 ASP 131 A LYS 132 n 104 LYS 132 A GLY 133 n 105 GLY 133 A LYS 134 n 106 LYS 134 A GLN 135 n 107 GLN 135 A TYR 136 n 108 TYR 136 A GLU 137 n 109 GLU 137 A LEU 138 n 110 LEU 138 A ASN 139 n 111 ASN 139 A TYR 140 n 112 TYR 140 A THR 141 n 113 THR 141 A PRO 142 n 114 PRO 142 A GLU 143 n 115 GLU 143 A SER 144 n 116 SER 144 A TYR 145 n 117 TYR 145 A GLY 146 n 118 GLY 146 A ASP 147 n 119 ASP 147 A LYS 148 n 120 LYS 148 A LYS 149 n 121 LYS 149 A PRO 150 n 122 PRO 150 A LYS 151 n 123 LYS 151 A SER 152 n 124 SER 152 A VAL 153 n 125 VAL 153 A THR 154 n 126 THR 154 A PHE 155 n 127 PHE 155 A LYS 156 n 128 LYS 156 A ILE 157 n 129 ILE 157 A ASP 158 n 130 ASP 158 A GLY 159 n 131 GLY 159 A LYS 160 n 132 LYS 160 A ASP 161 n 133 ASP 161 A LYS 162 n 134 LYS 162 A LYS 163 n 135 LYS 163 A ILE 164 n 136 ILE 164 A LEU 165 n 137 LEU 165 A ALA 166 n 138 ALA 166 A THR 167 n 139 THR 167 A ALA 168 n 140 ALA 168 A ASP 169 n 141 ASP 169 A LYS 170 n 142 LYS 170 A LEU 171 n 143 LEU 171 A GLN 172 n 144 GLN 172 A ASP 173 n 145 ASP 173 A SER 174 n 146 SER 174 A ALA 175 n 147 ALA 175 A LYS 176 n 148 LYS 176 A ALA 177 n 149 ALA 177 A LEU 178 n 150 LEU 178 A SER 179 n 151 SER 179 A ALA 180 n 152 ALA 180 A TYR 181 n 153 TYR 181 A VAL 182 n 154 VAL 182 A ASP 183 n 155 ASP 183 A VAL 184 n 156 VAL 184 A LEU 185 n 157 LEU 185 A LEU 186 n 158 LEU 186 A PHE 187 n 159 PHE 187 A GLY 188 n 160 GLY 188 A LYS 189 n 161 LYS 189 A ASP 190 n 162 ASP 190 A ASN 191 n 163 ASN 191 A ALA 192 n 164 ALA 192 A ASP 193 n 165 ASP 193 A PHE 194 n 166 PHE 194 A GLU 195 n 167 GLU 195 A LYS 196 n 168 LYS 196 A ILE 197 n 169 ILE 197 A THR 198 n 170 THR 198 A GLY 199 n 171 GLY 199 A ALA 200 n 172 ALA 200 A ASN 201 n 173 ASN 201 A LYS 202 n 174 LYS 202 A ASN 203 n 175 ASN 203 A GLU 204 n 176 GLU 204 A ILE 205 n 177 ILE 205 A VAL 206 n 178 VAL 206 A ASN 207 n 179 ASN 207 A ASP 208 n 180 ASP 208 A PHE 209 n 181 PHE 209 A ASN 210 n 182 ASN 210 A GLU 211 n 183 GLU 211 A SER 212 n 184 SER 212 A ALA 213 n 185 ALA 213 A LYS 214 n 186 LYS 214 A ASP 215 n 187 ASP 215 A GLY 216 n 188 GLY 216 A TYR 217 n 189 TYR 217 A LEU 218 n 190 LEU 218 A SER 219 n 191 SER 219 A ALA 220 n 192 ALA 220 A SER 221 n 193 SER 221 A GLY 222 n 194 GLY 222 A LEU 223 n 195 LEU 223 A SER 224 n 196 SER 224 A SER 225 n 197 SER 225 A THR 226 n 198 THR 226 A TYR 227 n 199 TYR 227 A ALA 228 n 200 ALA 228 A ASP 229 n 201 ASP 229 A SER 230 n 202 SER 230 A LYS 231 n 203 LYS 231 A ALA 232 n 204 ALA 232 A LEU 233 n 205 LEU 233 A ASP 234 n 206 ASP 234 A ASN 235 n 207 ASN 235 A ILE 236 n 208 ILE 236 A VAL 237 n 209 VAL 237 A ASN 238 n 210 ASN 238 A GLY 239 n 211 GLY 239 A ILE 240 n 212 ILE 240 A LYS 241 n 213 LYS 241 A GLU 242 n 214 GLU 242 A GLY 243 n 215 GLY 243 A LEU 244 n 216 LEU 244 A SER 245 n 217 SER 245 A LYS 246 n 218 LYS 246 A ASN 247 n 219 ASN 247 A SER 248 n 220 SER 248 A SER 249 n 221 SER 249 A ILE 250 n 222 ILE 250 A GLN 251 n 223 GLN 251 A ALA 252 n 224 ALA 252 A LYS 253 n 225 LYS 253 A THR 254 n 226 THR 254 A THR 255 n 227 THR 255 A SER 256 n 228 SER 256 A ILE 257 n 229 ILE 257 A SER 258 n 230 SER 258 A LYS 259 n 231 LYS 259 A ASP 260 n 232 ASP 260 A GLU 261 n 233 GLU 261 A ALA 262 n 234 ALA 262 A ILE 263 n 235 ILE 263 A VAL 264 n 236 VAL 264 A GLU 265 n 237 GLU 265 A ALA 266 n 238 ALA 266 A THR 267 n 239 THR 267 A VAL 268 n 240 VAL 268 A LYS 269 n 241 LYS 269 A PRO 270 n 242 PRO 270 A VAL 271 n 243 VAL 271 A ASP 272 n 244 ASP 272 A ALA 273 n 245 ALA 273 A SER 274 n 246 SER 274 A SER 275 n 247 SER 275 A LEU 276 n 248 LEU 276 A SER 277 n 249 SER 277 A ASP 278 n 250 ASP 278 A ARG 279 n 251 ARG 279 A ILE 280 n 252 ILE 280 A GLU 281 n 253 GLU 281 A ASP 282 n 254 ASP 282 A LYS 283 n 255 LYS 283 A VAL 284 n 256 VAL 284 A LYS 285 n 257 LYS 285 A ASP 286 n 258 ASP 286 A TYR 287 n 259 TYR 287 A TYR 288 n 260 TYR 288 A SER 289 n 261 SER 289 A LYS 290 n 262 LYS 290 A ASN 291 n 263 ASN 291 A SER 292 n 264 SER 292 A SER 293 n 265 SER 293 A ALA 294 n 266 ALA 294 A SER 295 n 267 SER 295 A TYR 296 n 268 TYR 296 A GLU 297 n 269 GLU 297 A GLU 298 n 270 GLU 298 A ALA 299 n 271 ALA 299 A VAL 300 n 272 VAL 300 A LYS 301 n 273 LYS 301 A TYR 302 n 274 TYR 302 A ALA 303 n 275 ALA 303 A LEU 304 n 276 LEU 304 A GLN 305 n 277 GLN 305 A VAL 306 n 278 VAL 306 A TYR 307 n 279 TYR 307 A PRO 308 n 280 PRO 308 A GLU 309 n 281 GLU 309 A GLU 310 n 282 GLU 310 A PHE 311 n 283 PHE 311 A LYS 312 n 284 LYS 312 A LYS 313 n 285 LYS 313 A LEU 314 n 286 LEU 314 A GLY 315 n 287 GLY 315 A PRO 316 n 288 PRO 316 A ALA 317 n 289 ALA 317 A SER 318 n 290 SER 318 A SER 319 n 291 SER 319 A GLU 320 n 292 GLU 320 A LYS 321 n 293 LYS 321 A THR 322 n 294 THR 322 A VAL 323 n 295 VAL 323 A GLU 324 n 296 GLU 324 A VAL 325 n 297 VAL 325 A LYS 326 n 298 LYS 326 A MSE 327 n 299 MSE 327 A LYS 328 n 300 LYS 328 A LYS 329 n 301 LYS 329 A ASN 330 n 302 ASN 330 A ASP 331 n 303 ASP 331 A ILE 332 n 304 ILE 332 A ASP 333 n 305 ASP 333 A GLN 334 n 306 GLN 334 A TRP 335 n 307 TRP 335 A GLN 336 n 308 GLN 336 A LEU 337 n 309 LEU 337 A ASP 338 n 310 ASP 338 A MSE 339 n 311 MSE 339 A ASP 340 n 312 ASP 340 A ASP 341 n 313 ASP 341 A TYR 342 n 314 TYR 342 A ARG 343 n 315 ARG 343 A ALA 344 n 316 ALA 344 A ALA 345 n 317 ALA 345 A GLU 346 n 318 GLU 346 A LEU 347 n 319 LEU 347 A VAL 348 n 320 VAL 348 A GLU 349 n 321 GLU 349 A ALA 350 n 322 ALA 350 A PHE 351 n 323 PHE 351 A ILE 352 n 324 ILE 352 A LYS 353 n 325 LYS 353 A GLU 354 n 326 GLU 354 A 0.6088 -0.0593 2.0175 0.5434 0.7999 8.3155 -0.2117 -0.0877 0.0287 0.1853 0.1074 0.0081 -0.4138 -0.3718 0.1043 -0.1615 0.0897 -0.1061 0.0414 -0.0160 -0.1197 refined 1.5638 39.7534 86.9264 X-RAY DIFFRACTION A 33 A 354 X-RAY DIFFRACTION 1 {A|33 - 354} author_and_software_defined_assembly PISA 1 monomeric A MSE 88 SELENOMETHIONINE A MSE 60 MET A MSE 99 SELENOMETHIONINE A MSE 71 MET A MSE 327 SELENOMETHIONINE A MSE 299 MET A MSE 339 SELENOMETHIONINE A MSE 311 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 N LYS 38 A N LYS 10 A O VAL 45 A O VAL 17 A N SER 51 A N SER 23 A O LYS 70 A O LYS 42 A N LEU 69 A N LEU 41 A O PHE 128 A O PHE 100 A N LEU 83 A N LEU 55 A O ILE 116 A O ILE 88 A O THR 97 A O THR 69 A N GLN 94 A N GLN 66 A N THR 91 A N THR 63 A O ASN 139 A O ASN 111 A N LEU 138 A N LEU 110 A O PHE 155 A O PHE 127 A N LYS 253 A N LYS 225 A O GLU 265 A O GLU 237 A N VAL 268 A N VAL 240 A O LYS 321 A O LYS 293 A N LYS 328 A N LYS 300 A O GLN 336 A O GLN 308 A N VAL 271 A N VAL 243 A O LYS 353 A O LYS 325 1 A CG LYS 80 A CG LYS 52 1 Y 1 A CD LYS 80 A CD LYS 52 1 Y 1 A CE LYS 80 A CE LYS 52 1 Y 1 A NZ LYS 80 A NZ LYS 52 1 Y 1 A CG TYR 145 A CG TYR 117 1 Y 1 A CD1 TYR 145 A CD1 TYR 117 1 Y 1 A CD2 TYR 145 A CD2 TYR 117 1 Y 1 A CE1 TYR 145 A CE1 TYR 117 1 Y 1 A CE2 TYR 145 A CE2 TYR 117 1 Y 1 A CZ TYR 145 A CZ TYR 117 1 Y 1 A OH TYR 145 A OH TYR 117 1 Y 1 A OG SER 224 A OG SER 196 1 Y 1 A OG SER 225 A OG SER 197 1 Y 1 A CG TYR 342 A CG TYR 314 1 Y 1 A CD1 TYR 342 A CD1 TYR 314 1 Y 1 A CD2 TYR 342 A CD2 TYR 314 1 Y 1 A CE1 TYR 342 A CE1 TYR 314 1 Y 1 A CE2 TYR 342 A CE2 TYR 314 1 Y 1 A CZ TYR 342 A CZ TYR 314 1 Y 1 A OH TYR 342 A OH TYR 314 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A GLU 30 A GLU 2 1 Y 1 A LYS 31 A LYS 3 1 Y 1 A LYS 32 A LYS 4 1 Y 1 A LYS 80 -100.93 -63.63 1 A ASN 191 -166.13 93.69 1 A TYR 227 -53.86 -9.70 1 A ASP 229 -111.59 71.39 1 A LYS 259 65.70 -114.23 1 A LYS 290 -84.49 -75.00 1 A SER 293 -76.48 37.63 166.830 89.4081 49.680 -13.4645 0.0000 0.0000 -13.4645 0.0000 26.9289 0.9180 0.9075 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. PEG (PG4) MODELED WERE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 0.2389 0.2135 0.2147 2.6200 49.327 889 17574 5.0600 99.8700 1.000 0.370 RANDOM 1 THROUGHOUT 0.000 MAD 0.506 2.6200 49.327 33 2557 39 0 2485 1282 SINUSOIDAL 2.000 89 HARMONIC 2.000 358 HARMONIC 5.000 2586 HARMONIC 20.000 346 SEMIHARMONIC 5.000 2830 SEMIHARMONIC 4.000 0.010 2586 HARMONIC 2.000 1.210 3479 HARMONIC 2.000 3.080 3.120 0.2875 0.2574 0.2591 2.7800 156 2600 2756 9 5.6600 99.8700 84.781 2.62 49.327 4R4G 17632 -3.000 0.090 1 22.880 99.800 0.906 0.023 2.620 2.710 1.8 21199 1640 1638 2.396 1 99.900 0.888 0.023 2.710 2.820 2.5 20805 1753 1745 1.526 1 99.500 0.959 0.023 2.820 2.950 4.0 23416 1749 1744 0.926 1 99.700 0.985 0.023 2.950 3.100 6.4 22234 1667 1667 0.553 1 100.000 0.992 0.023 3.100 3.300 10.2 23782 1795 1794 0.310 1 99.900 0.997 0.023 3.300 3.550 16.8 21857 1709 1706 0.171 1 99.800 0.999 0.023 3.550 3.910 25.5 21926 1771 1769 0.095 1 99.900 0.999 0.023 3.910 4.470 39.4 23315 1772 1772 0.062 1 100.000 1.000 0.023 4.470 5.610 48.6 21313 1793 1790 0.047 1 99.800 1.000 0.023 5.610 64.8 23313 2007 1992 0.031 1 99.300 model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data extraction PDB deposit@deposit.rcsb.org June 10, 2010 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.10 phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package phasing Eric de La Fortelle sharp-develop@globalphasing.com http://www.globalphasing.com/sharp/ SHARP package data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package January 10, 2014 BUILT=20140307 refinement Gerard Bricogne buster-develop@GlobalPhasing.com http://www.globalphasing.com/buster/ BUSTER-TNT program 2.10.0 data reduction XDS phasing SHELXD refinement BUSTER 2.10.0 Crystal structure of a putative lipoprotein (ycdA) from Bacillus subtilis subsp. subtilis str. 168 at 2.62 A resolution 1 N N 2 N N 2 N N 2 N N 3 N N CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. A ASP 86 A ASP 58 HELX_P A MSE 88 A MSE 60 5 1 3 A ASP 106 A ASP 78 HELX_P A LYS 110 A LYS 82 5 2 5 A ASP 147 A ASP 119 HELX_P A SER 152 A SER 124 1 3 6 A ASP 161 A ASP 133 HELX_P A LYS 170 A LYS 142 1 4 10 A GLN 172 A GLN 144 HELX_P A LEU 186 A LEU 158 1 5 15 A ALA 192 A ALA 164 HELX_P A GLY 199 A GLY 171 1 6 8 A ASN 201 A ASN 173 HELX_P A SER 221 A SER 193 1 7 21 A SER 224 A SER 196 HELX_P A ASP 229 A ASP 201 5 8 6 A SER 230 A SER 202 HELX_P A SER 248 A SER 220 1 9 19 A SER 275 A SER 247 HELX_P A SER 289 A SER 261 1 10 15 A SER 295 A SER 267 HELX_P A LYS 312 A LYS 284 1 11 18 A ASP 341 A ASP 313 HELX_P A ALA 350 A ALA 322 1 12 10 covale 1.375 both A SER 87 A C SER 59 1_555 A MSE 88 A N MSE 60 1_555 covale 1.346 both A MSE 88 A C MSE 60 1_555 A ASP 89 A N ASP 61 1_555 covale 1.345 both A LYS 98 A C LYS 70 1_555 A MSE 99 A N MSE 71 1_555 covale 1.329 both A MSE 99 A C MSE 71 1_555 A SER 100 A N SER 72 1_555 covale 1.335 both A LYS 326 A C LYS 298 1_555 A MSE 327 A N MSE 299 1_555 covale 1.337 both A MSE 327 A C MSE 299 1_555 A LYS 328 A N LYS 300 1_555 covale 1.335 both A ASP 338 A C ASP 310 1_555 A MSE 339 A N MSE 311 1_555 covale 1.343 both A MSE 339 A C MSE 311 1_555 A ASP 340 A N ASP 312 1_555 STRUCTURAL GENOMICS, UNKNOWN FUNCTION Two domain protein, N-terminal domain has Ig-like fold, belongs to DUF4352 family (PF11611), C-terminal domain has fold: alpha(2)-beta(2)-alpha(2)-beta-alpha; domains connected by kinked-helix, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-BIOLOGY, UNKNOWN FUNCTION YCDA_BACSU UNP 1 30 O34538 EKKESETEKSSDIAQVKIKDVSYTLPSKYDKSTSDDQLVLKVNVAVKNTGKDPLNVDSMDFTLYQGDTKMSDTDPEDYSE KLQGSTINADKSVEGNLFFVVDKGKQYELNYTPESYGDKKPKSVTFKIDGKDKKILATADKLQDSAKALSAYVDVLLFGK DNADFEKITGANKNEIVNDFNESAKDGYLSASGLSSTYADSKALDNIVNGIKEGLSKNSSIQAKTTSISKDEAIVEATVK PVDASSLSDRIEDKVKDYYSKNSSASYEEAVKYALQVYPEEFKKLGPASSEKTVEVKMKKNDIDQWQLDMDDYRAAELVE AFIKE 30 354 4R4G 30 354 O34538 A 1 2 326 1 expression tag GLY 0 4R4G A O34538 UNP 1 4 2 4 4 2 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel A GLU 37 A GLU 9 A SER 39 A SER 11 A GLN 44 A GLN 16 A THR 53 A THR 25 A LEU 67 A LEU 39 A LYS 76 A LYS 48 A SER 121 A SER 93 A VAL 130 A VAL 102 A LEU 83 A LEU 55 A VAL 85 A VAL 57 A SER 114 A SER 86 A ILE 116 A ILE 88 A THR 97 A THR 69 A MSE 99 A MSE 71 A PHE 90 A PHE 62 A GLN 94 A GLN 66 A GLN 135 A GLN 107 A TYR 140 A TYR 112 A VAL 153 A VAL 125 A ASP 158 A ASP 130 A SER 249 A SER 221 A SER 258 A SER 230 A GLU 261 A GLU 233 A LYS 269 A LYS 241 A LYS 321 A LYS 293 A LYS 329 A LYS 301 A TRP 335 A TRP 307 A GLN 336 A GLN 308 A VAL 271 A VAL 243 A ASP 272 A ASP 244 A ILE 352 A ILE 324 A LYS 353 A LYS 325 BINDING SITE FOR RESIDUE PG4 A 401 A PG4 401 Software 5 BINDING SITE FOR RESIDUE PG4 A 402 A PG4 402 Software 4 BINDING SITE FOR RESIDUE PG4 A 403 A PG4 403 Software 3 A TYR 93 A TYR 65 5 11_555 A GLU 137 A GLU 109 5 11_555 A ASN 139 A ASN 111 5 11_555 A ASN 139 A ASN 111 5 1_555 A LYS 149 A LYS 121 5 1_555 A LEU 54 A LEU 26 4 1_555 A ASP 64 A ASP 36 4 1_555 A LYS 253 A LYS 225 4 1_555 A THR 255 A THR 227 4 1_555 A ALA 213 A ALA 185 3 1_555 A ILE 240 A ILE 212 3 1_555 A VAL 348 A VAL 320 3 1_555 179 P 65 2 2