0.017553 0.000000 0.006708 0.000000 0.019656 0.000000 0.000000 0.000000 0.014554 0.000000 0.000000 0.000000 Shen, Y. Tong, Y. Sukumar, D. Tempel, W. Loppnau, P. Arrowsmith, C.H. Edwards, A.M. Bountra, C. Wilkstrom, M. Bochkarev, A. Park, H. Structural Genomics Consortium (SGC) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 110.910 90.000 56.969 50.875 73.553 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 C10 H15 N5 O11 P2 443.201 n GUANOSINE-5'-DIPHOSPHATE RNA 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 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 C5 H11 N O2 S 149.211 y METHIONINE 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 UNKNOWN ATOM OR ION non-polymer C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 S C N 16 N C N 17 N O N 18 N C N 19 N C N 20 N C N 21 N N N 22 N C N 23 N N N 24 N N N 25 N O N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N H N 37 N H N 38 N H N 39 N H N 40 N H N 41 N N N 42 S C N 43 N C N 44 N O N 45 N C N 46 N C N 47 N O N 48 N N N 49 N O N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N H N 56 N H N 57 N H N 58 N N N 59 S C N 60 N C N 61 N O N 62 N C N 63 N C N 64 N O N 65 N O N 66 N O N 67 N H N 68 N H N 69 N H N 70 N H N 71 N H N 72 N H N 73 N H N 74 N N N 75 R C N 76 N C N 77 N O N 78 N C N 79 N S N 80 N O N 81 N H N 82 N H N 83 N H N 84 N H N 85 N H N 86 N H N 87 N H N 88 N P N 89 N O N 90 N O N 91 N O N 92 N O N 93 N P N 94 N O N 95 N O N 96 N O N 97 N C N 98 R C N 99 N O N 100 S C N 101 N O N 102 R C N 103 N O N 104 R C Y 105 N N Y 106 N C Y 107 N N Y 108 N C N 109 N C N 110 N O N 111 N N N 112 N C N 113 N N N 114 N N Y 115 N C N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N H N 131 N N N 132 S C N 133 N C N 134 N O N 135 N C N 136 N C N 137 N C N 138 N O N 139 N N N 140 N O N 141 N H N 142 N H N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N N N 152 S C N 153 N C N 154 N O N 155 N C N 156 N C N 157 N C N 158 N O N 159 N O N 160 N O N 161 N H N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N N N 171 N C N 172 N C N 173 N O N 174 N O N 175 N H N 176 N H N 177 N H N 178 N H N 179 N H N 180 N N N 181 S C N 182 N C N 183 N O N 184 N C Y 185 N C Y 186 N N Y 187 N C Y 188 N C Y 189 N N N 190 N O N 191 N H N 192 N H N 193 N H N 194 N H N 195 N H N 196 N H N 197 N H N 198 N H N 199 N H N 200 N H N 201 N O N 202 N H N 203 N H N 204 N N N 205 S C N 206 N C N 207 N O N 208 S C N 209 N C N 210 N C N 211 N C N 212 N O N 213 N H N 214 N H N 215 N H N 216 N H N 217 N H N 218 N H N 219 N H N 220 N H N 221 N H N 222 N H N 223 N H N 224 N H N 225 N H N 226 N N N 227 S C N 228 N C N 229 N O N 230 N C N 231 N C N 232 N C N 233 N C N 234 N O N 235 N H N 236 N H N 237 N H N 238 N H N 239 N H N 240 N H N 241 N H N 242 N H N 243 N H N 244 N H N 245 N H N 246 N H N 247 N H N 248 N N N 249 S C N 250 N C N 251 N O N 252 N C N 253 N C N 254 N C N 255 N C N 256 N N N 257 N O N 258 N H N 259 N H N 260 N H N 261 N H N 262 N H N 263 N H N 264 N H N 265 N H N 266 N H N 267 N H N 268 N H N 269 N H N 270 N H N 271 N H N 272 N H N 273 N N N 274 S C N 275 N C N 276 N O N 277 N C N 278 N C N 279 N S N 280 N C N 281 N O N 282 N H N 283 N H N 284 N H N 285 N H N 286 N H N 287 N H N 288 N H N 289 N H N 290 N H N 291 N H N 292 N H N 293 N N N 294 S C N 295 N C N 296 N O N 297 N C Y 298 N C Y 299 N C Y 300 N C Y 301 N C Y 302 N C Y 303 N C N 304 N O N 305 N H N 306 N H N 307 N H N 308 N H N 309 N H N 310 N H N 311 N H N 312 N H N 313 N H N 314 N H N 315 N H N 316 N N N 317 S C N 318 N C N 319 N O N 320 N C N 321 N C N 322 N C N 323 N O N 324 N H N 325 N H N 326 N H N 327 N H N 328 N H N 329 N H N 330 N H N 331 N H N 332 N H N 333 N N N 334 S C N 335 N C N 336 N O N 337 N C N 338 N O N 339 N O N 340 N H N 341 N H N 342 N H N 343 N H N 344 N H N 345 N H N 346 N H N 347 N N N 348 S C N 349 N C N 350 N O N 351 R C N 352 N O N 353 N C N 354 N O N 355 N H N 356 N H N 357 N H N 358 N H N 359 N H N 360 N H N 361 N H N 362 N H N 363 N H N 364 N N N 365 S C N 366 N C N 367 N O N 368 N C Y 369 N C Y 370 N C Y 371 N C Y 372 N N Y 373 N C Y 374 N C Y 375 N C Y 376 N C Y 377 N C N 378 N O N 379 N H N 380 N H N 381 N H N 382 N H N 383 N H N 384 N H N 385 N H N 386 N H N 387 N H N 388 N H N 389 N H N 390 N H N 391 N N N 392 S C N 393 N C N 394 N O N 395 N C Y 396 N C Y 397 N C Y 398 N C Y 399 N C Y 400 N C Y 401 N C N 402 N O N 403 N O N 404 N H N 405 N H N 406 N H N 407 N H N 408 N H N 409 N H N 410 N H N 411 N H N 412 N H N 413 N H N 414 N H N 415 N N N 416 S C N 417 N C N 418 N O N 419 N C N 420 N C N 421 N C N 422 N O N 423 N H N 424 N H N 425 N H N 426 N H N 427 N H N 428 N H N 429 N H N 430 N H N 431 N H N 432 N H N 433 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N doub N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N sing N 32 N sing N 33 N doub N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N doub N 46 N sing N 47 N sing N 48 N sing N 49 N sing N 50 N doub N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N doub N 62 N sing N 63 N sing N 64 N sing N 65 N sing N 66 N doub N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N doub N 77 N sing N 78 N sing N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N doub N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N sing N 89 N sing N 90 N doub N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N sing N 103 N sing N 104 N sing N 105 N sing N 106 N sing N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing Y 112 N sing Y 113 N sing Y 114 N doub N 115 N sing Y 116 N sing N 117 N sing Y 118 N doub N 119 N doub N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N doub N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N doub N 135 N sing N 136 N sing N 137 N sing N 138 N sing N 139 N sing N 140 N sing N 141 N sing N 142 N doub N 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N doub N 154 N sing N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N doub N 162 N sing N 163 N sing N 164 N sing N 165 N sing N 166 N sing N 167 N sing N 168 N sing N 169 N sing N 170 N sing N 171 N doub N 172 N sing N 173 N sing N 174 N sing N 175 N sing N 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N doub N 181 N sing N 182 N sing N 183 N sing N 184 N sing Y 185 N sing Y 186 N doub Y 187 N doub N 188 N sing Y 189 N sing N 190 N sing Y 191 N sing N 192 N sing N 193 N sing N 194 N sing N 195 N sing N 196 N sing N 197 N sing N 198 N sing N 199 N sing N 200 N sing N 201 N sing N 202 N sing N 203 N doub N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N sing N 210 N sing N 211 N sing N 212 N sing N 213 N sing N 214 N sing N 215 N sing N 216 N sing N 217 N sing N 218 N sing N 219 N sing N 220 N sing N 221 N sing N 222 N sing N 223 N sing N 224 N doub N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N sing N 231 N sing N 232 N sing N 233 N sing N 234 N sing N 235 N sing N 236 N sing N 237 N sing N 238 N sing N 239 N sing N 240 N sing N 241 N sing N 242 N sing N 243 N sing N 244 N sing N 245 N doub N 246 N sing N 247 N sing N 248 N sing N 249 N sing N 250 N sing N 251 N sing N 252 N sing N 253 N sing N 254 N sing N 255 N sing N 256 N sing N 257 N sing N 258 N sing N 259 N sing N 260 N sing N 261 N sing N 262 N sing N 263 N sing N 264 N sing N 265 N sing N 266 N sing N 267 N sing N 268 N sing N 269 N doub N 270 N sing N 271 N sing N 272 N sing N 273 N sing N 274 N sing N 275 N sing N 276 N sing N 277 N sing N 278 N sing N 279 N sing N 280 N sing N 281 N sing N 282 N sing N 283 N sing N 284 N sing N 285 N sing N 286 N sing N 287 N sing N 288 N doub N 289 N sing N 290 N sing N 291 N sing N 292 N sing Y 293 N doub Y 294 N sing Y 295 N sing N 296 N sing Y 297 N doub N 298 N sing Y 299 N doub N 300 N sing Y 301 N sing N 302 N sing N 303 N sing N 304 N sing N 305 N sing N 306 N sing N 307 N sing N 308 N sing N 309 N sing N 310 N sing N 311 N doub N 312 N sing N 313 N sing N 314 N sing N 315 N sing N 316 N sing N 317 N sing N 318 N sing N 319 N sing N 320 N sing N 321 N sing N 322 N sing N 323 N sing N 324 N sing N 325 N sing N 326 N sing N 327 N sing N 328 N doub N 329 N sing N 330 N sing N 331 N sing N 332 N sing N 333 N sing N 334 N sing N 335 N sing N 336 N sing N 337 N sing N 338 N sing N 339 N sing N 340 N sing N 341 N doub N 342 N sing N 343 N sing N 344 N sing N 345 N sing N 346 N sing N 347 N sing N 348 N sing N 349 N sing N 350 N sing N 351 N sing N 352 N sing N 353 N sing N 354 N sing N 355 N sing N 356 N sing N 357 N doub N 358 N sing N 359 N sing N 360 N sing N 361 N sing Y 362 N doub Y 363 N sing Y 364 N sing N 365 N sing Y 366 N doub Y 367 N sing Y 368 N sing N 369 N sing Y 370 N sing Y 371 N doub N 372 N sing Y 373 N doub N 374 N sing Y 375 N sing N 376 N sing N 377 N sing N 378 N sing N 379 N sing N 380 N sing N 381 N sing N 382 N sing N 383 N sing N 384 N sing N 385 N doub N 386 N sing N 387 N sing N 388 N sing N 389 N sing Y 390 N doub Y 391 N sing Y 392 N sing N 393 N sing Y 394 N doub N 395 N sing Y 396 N doub N 397 N sing Y 398 N sing N 399 N sing N 400 N sing N 401 N sing N 402 N sing N 403 N sing N 404 N sing N 405 N sing N 406 N sing N 407 N sing N 408 N sing N 409 N doub N 410 N sing N 411 N sing N 412 N sing N 413 N sing N 414 N sing N 415 N sing N 416 N sing N 417 N sing N 418 N sing N 419 N sing N 420 N sing To be Published 0353 Crystal structure of human Rab3B GTPase bound with GDP 10.2210/pdb3dz8/pdb pdb_00003dz8 100 1 IMAGE PLATE 2008-05-13 RIGAKU RAXIS SINGLE WAVELENGTH M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU FR-E DW 22182.936 Ras-related protein Rab-3B UNP residues 18-190 1 man polymer 443.201 GUANOSINE-5'-DIPHOSPHATE 1 syn non-polymer UNKNOWN ATOM OR ION 6 syn non-polymer 18.015 water 30 nat water no no MHHHHHHSSGRENLYFQGNFDYMFKLLIIGNSSVGKTSFLFRYADDTFTPAFVSTVGIDFKVKTVYRHEKRVKLQIWDTA GQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEEERVVPTEKGQLLAEQLGF DFFEASAKENISVRQAFERLVDAICDKMSDS MHHHHHHSSGRENLYFQGNFDYMFKLLIIGNSSVGKTSFLFRYADDTFTPAFVSTVGIDFKVKTVYRHEKRVKLQIWDTA GQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEEERVVPTEKGQLLAEQLGF DFFEASAKENISVRQAFERLVDAICDKMSDS A 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 Human sample RAB3B 9606 Homo sapiens 562 Escherichia coli BL21-CodonPlus(DE3)-V2R pET28-mhl (GI:134105571) 1 2.4 48.5 VAPOR DIFFUSION, SITTING DROP 7.5 2M ammonium sulfate, 0.2M sodium acetate, 0.1M HEPES, 5% MPD, pH 7.5, vapor diffusion, sitting drop, temperature 291K 291 Structural Genomics Consortium SGC software chem_comp_atom chem_comp_bond database_2 pdbx_initial_refinement_model struct_ref_seq_dif struct_site repository Initial release Advisory Version format compliance Refinement description Data collection Database references Derived calculations Refinement description 1 0 2008-08-12 1 1 2011-07-13 1 2 2017-10-25 1 3 2023-08-30 _software.classification _software.contact_author _software.contact_author_email _software.date _software.language _software.location _software.name _software.type _software.version _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 2008-07-29 REL REL GDP GUANOSINE-5'-DIPHOSPHATE UNX UNKNOWN ATOM OR ION HOH water 2GF9 PDB ENTRY 2GF9 PDB experimental model GDP 201 2 GDP GDP 201 A UNX 501 3 UNX UNX 501 A UNX 502 3 UNX UNX 502 A UNX 503 3 UNX UNX 503 A UNX 504 3 UNX UNX 504 A UNX 505 3 UNX UNX 505 A UNX 506 3 UNX UNX 506 A HOH 1 4 HOH HOH 507 A HOH 2 4 HOH HOH 508 A HOH 3 4 HOH HOH 509 A HOH 4 4 HOH HOH 510 A HOH 5 4 HOH HOH 511 A HOH 6 4 HOH HOH 512 A HOH 7 4 HOH HOH 513 A HOH 8 4 HOH HOH 514 A HOH 9 4 HOH HOH 515 A HOH 10 4 HOH HOH 516 A HOH 11 4 HOH HOH 517 A HOH 12 4 HOH HOH 518 A HOH 13 4 HOH HOH 519 A HOH 14 4 HOH HOH 520 A HOH 15 4 HOH HOH 521 A HOH 16 4 HOH HOH 522 A HOH 17 4 HOH HOH 523 A HOH 18 4 HOH HOH 524 A HOH 19 4 HOH HOH 525 A HOH 20 4 HOH HOH 526 A HOH 21 4 HOH HOH 527 A HOH 22 4 HOH HOH 528 A HOH 23 4 HOH HOH 529 A HOH 24 4 HOH HOH 530 A HOH 25 4 HOH HOH 531 A HOH 26 4 HOH HOH 532 A HOH 27 4 HOH HOH 533 A HOH 28 4 HOH HOH 534 A HOH 29 4 HOH HOH 535 A HOH 30 4 HOH HOH 536 A n 1 0 A n 2 1 A n 3 2 A n 4 3 A n 5 4 A n 6 5 A n 7 6 A n 8 7 A n 9 8 A n 10 9 A ARG 10 n 11 ARG 10 A GLU 11 n 12 GLU 11 A ASN 12 n 13 ASN 12 A LEU 13 n 14 LEU 13 A TYR 14 n 15 TYR 14 A PHE 15 n 16 PHE 15 A GLN 16 n 17 GLN 16 A GLY 17 n 18 GLY 17 A ASN 18 n 19 ASN 18 A PHE 19 n 20 PHE 19 A ASP 20 n 21 ASP 20 A TYR 21 n 22 TYR 21 A MET 22 n 23 MET 22 A PHE 23 n 24 PHE 23 A LYS 24 n 25 LYS 24 A LEU 25 n 26 LEU 25 A LEU 26 n 27 LEU 26 A ILE 27 n 28 ILE 27 A ILE 28 n 29 ILE 28 A GLY 29 n 30 GLY 29 A ASN 30 n 31 ASN 30 A SER 31 n 32 SER 31 A SER 32 n 33 SER 32 A VAL 33 n 34 VAL 33 A GLY 34 n 35 GLY 34 A LYS 35 n 36 LYS 35 A THR 36 n 37 THR 36 A SER 37 n 38 SER 37 A PHE 38 n 39 PHE 38 A LEU 39 n 40 LEU 39 A PHE 40 n 41 PHE 40 A ARG 41 n 42 ARG 41 A TYR 42 n 43 TYR 42 A ALA 43 n 44 ALA 43 A ASP 44 n 45 ASP 44 A ASP 45 n 46 ASP 45 A THR 46 n 47 THR 46 A PHE 47 n 48 PHE 47 A THR 48 n 49 THR 48 A PRO 49 n 50 PRO 49 A ALA 50 n 51 ALA 50 A PHE 51 n 52 PHE 51 A VAL 52 n 53 VAL 52 A SER 53 n 54 SER 53 A THR 54 n 55 THR 54 A VAL 55 n 56 VAL 55 A GLY 56 n 57 GLY 56 A ILE 57 n 58 ILE 57 A ASP 58 n 59 ASP 58 A PHE 59 n 60 PHE 59 A LYS 60 n 61 LYS 60 A VAL 61 n 62 VAL 61 A LYS 62 n 63 LYS 62 A THR 63 n 64 THR 63 A VAL 64 n 65 VAL 64 A TYR 65 n 66 TYR 65 A ARG 66 n 67 ARG 66 A HIS 67 n 68 HIS 67 A GLU 68 n 69 GLU 68 A LYS 69 n 70 LYS 69 A ARG 70 n 71 ARG 70 A VAL 71 n 72 VAL 71 A LYS 72 n 73 LYS 72 A LEU 73 n 74 LEU 73 A GLN 74 n 75 GLN 74 A ILE 75 n 76 ILE 75 A TRP 76 n 77 TRP 76 A ASP 77 n 78 ASP 77 A THR 78 n 79 THR 78 A ALA 79 n 80 ALA 79 A GLY 80 n 81 GLY 80 A GLN 81 n 82 GLN 81 A GLU 82 n 83 GLU 82 A ARG 83 n 84 ARG 83 A TYR 84 n 85 TYR 84 A ARG 85 n 86 ARG 85 A THR 86 n 87 THR 86 A ILE 87 n 88 ILE 87 A THR 88 n 89 THR 88 A THR 89 n 90 THR 89 A ALA 90 n 91 ALA 90 A TYR 91 n 92 TYR 91 A TYR 92 n 93 TYR 92 A ARG 93 n 94 ARG 93 A GLY 94 n 95 GLY 94 A ALA 95 n 96 ALA 95 A MET 96 n 97 MET 96 A GLY 97 n 98 GLY 97 A PHE 98 n 99 PHE 98 A ILE 99 n 100 ILE 99 A LEU 100 n 101 LEU 100 A MET 101 n 102 MET 101 A TYR 102 n 103 TYR 102 A ASP 103 n 104 ASP 103 A ILE 104 n 105 ILE 104 A THR 105 n 106 THR 105 A ASN 106 n 107 ASN 106 A GLU 107 n 108 GLU 107 A GLU 108 n 109 GLU 108 A SER 109 n 110 SER 109 A PHE 110 n 111 PHE 110 A ASN 111 n 112 ASN 111 A ALA 112 n 113 ALA 112 A VAL 113 n 114 VAL 113 A GLN 114 n 115 GLN 114 A ASP 115 n 116 ASP 115 A TRP 116 n 117 TRP 116 A ALA 117 n 118 ALA 117 A THR 118 n 119 THR 118 A GLN 119 n 120 GLN 119 A ILE 120 n 121 ILE 120 A LYS 121 n 122 LYS 121 A THR 122 n 123 THR 122 A TYR 123 n 124 TYR 123 A SER 124 n 125 SER 124 A TRP 125 n 126 TRP 125 A ASP 126 n 127 ASP 126 A ASN 127 n 128 ASN 127 A ALA 128 n 129 ALA 128 A GLN 129 n 130 GLN 129 A VAL 130 n 131 VAL 130 A ILE 131 n 132 ILE 131 A LEU 132 n 133 LEU 132 A VAL 133 n 134 VAL 133 A GLY 134 n 135 GLY 134 A ASN 135 n 136 ASN 135 A LYS 136 n 137 LYS 136 A CYS 137 n 138 CYS 137 A ASP 138 n 139 ASP 138 A MET 139 n 140 MET 139 A GLU 140 n 141 GLU 140 A GLU 141 n 142 GLU 141 A GLU 142 n 143 GLU 142 A ARG 143 n 144 ARG 143 A VAL 144 n 145 VAL 144 A VAL 145 n 146 VAL 145 A PRO 146 n 147 PRO 146 A THR 147 n 148 THR 147 A GLU 148 n 149 GLU 148 A LYS 149 n 150 LYS 149 A GLY 150 n 151 GLY 150 A GLN 151 n 152 GLN 151 A LEU 152 n 153 LEU 152 A LEU 153 n 154 LEU 153 A ALA 154 n 155 ALA 154 A GLU 155 n 156 GLU 155 A GLN 156 n 157 GLN 156 A LEU 157 n 158 LEU 157 A GLY 158 n 159 GLY 158 A PHE 159 n 160 PHE 159 A ASP 160 n 161 ASP 160 A PHE 161 n 162 PHE 161 A PHE 162 n 163 PHE 162 A GLU 163 n 164 GLU 163 A ALA 164 n 165 ALA 164 A SER 165 n 166 SER 165 A ALA 166 n 167 ALA 166 A LYS 167 n 168 LYS 167 A GLU 168 n 169 GLU 168 A ASN 169 n 170 ASN 169 A ILE 170 n 171 ILE 170 A SER 171 n 172 SER 171 A VAL 172 n 173 VAL 172 A ARG 173 n 174 ARG 173 A GLN 174 n 175 GLN 174 A ALA 175 n 176 ALA 175 A PHE 176 n 177 PHE 176 A GLU 177 n 178 GLU 177 A ARG 178 n 179 ARG 178 A LEU 179 n 180 LEU 179 A VAL 180 n 181 VAL 180 A ASP 181 n 182 ASP 181 A ALA 182 n 183 ALA 182 A ILE 183 n 184 ILE 183 A CYS 184 n 185 CYS 184 A ASP 185 n 186 ASP 185 A LYS 186 n 187 LYS 186 A MET 187 n 188 MET 187 A n 189 188 A n 190 189 A n 191 190 A 2.2491 -0.2879 1.0967 0.9063 -0.2367 3.9417 0.0117 0.5953 0.0624 -0.1411 -0.0209 -0.1674 0.1075 0.2952 0.0091 0.0998 -0.0017 0.0118 0.1620 0.0134 0.1222 refined 14.0635 7.9495 19.0319 X-RAY DIFFRACTION 2.6703 -0.5362 1.5328 6.8177 5.6964 10.1764 0.0801 0.1975 -0.1697 0.1134 -0.2703 0.4493 0.2552 -0.6368 0.1902 0.0583 -0.0124 -0.0313 0.1148 -0.0085 0.0726 refined 0.1834 6.3456 16.9318 X-RAY DIFFRACTION A 10 A 11 A 187 A 188 X-RAY DIFFRACTION 1 A 201 B A 201 B X-RAY DIFFRACTION 2 software_defined_assembly PISA 2 dimeric 3890 -19 15190 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_656 -x+1,y,-z+1 crystal symmetry operation 30.7178575603 0.0000000000 68.7089610576 A N LEU 13 A N LEU 14 A O ASP 20 A O ASP 21 A N VAL 55 A N VAL 56 A O PHE 59 A O PHE 60 A N VAL 64 A N VAL 65 A O LEU 73 A O LEU 74 A O LYS 72 A O LYS 73 A N LEU 25 A N LEU 26 A N ILE 28 A N ILE 29 A O MET 101 A O MET 102 A N TYR 102 A N TYR 103 A O ASN 135 A O ASN 136 A N LEU 132 A N LEU 133 A O ASP 160 A O ASP 161 1 A CG TYR 21 A CG TYR 22 1 Y 1 A CD1 TYR 21 A CD1 TYR 22 1 Y 1 A CD2 TYR 21 A CD2 TYR 22 1 Y 1 A CE1 TYR 21 A CE1 TYR 22 1 Y 1 A CE2 TYR 21 A CE2 TYR 22 1 Y 1 A CZ TYR 21 A CZ TYR 22 1 Y 1 A OH TYR 21 A OH TYR 22 1 Y 1 A CG PHE 47 A CG PHE 48 1 Y 1 A CD1 PHE 47 A CD1 PHE 48 1 Y 1 A CD2 PHE 47 A CD2 PHE 48 1 Y 1 A CE1 PHE 47 A CE1 PHE 48 1 Y 1 A CE2 PHE 47 A CE2 PHE 48 1 Y 1 A CZ PHE 47 A CZ PHE 48 1 Y 1 A CG GLU 68 A CG GLU 69 1 Y 1 A CD GLU 68 A CD GLU 69 1 Y 1 A OE1 GLU 68 A OE1 GLU 69 1 Y 1 A OE2 GLU 68 A OE2 GLU 69 1 Y 1 A CE LYS 69 A CE LYS 70 1 Y 1 A NZ LYS 69 A NZ LYS 70 1 Y 1 A CD ARG 85 A CD ARG 86 1 Y 1 A NE ARG 85 A NE ARG 86 1 Y 1 A CZ ARG 85 A CZ ARG 86 1 Y 1 A NH1 ARG 85 A NH1 ARG 86 1 Y 1 A NH2 ARG 85 A NH2 ARG 86 1 Y 1 A CD GLU 108 A CD GLU 109 1 Y 1 A OE1 GLU 108 A OE1 GLU 109 1 Y 1 A OE2 GLU 108 A OE2 GLU 109 1 Y 1 A CG GLN 114 A CG GLN 115 1 Y 1 A CD GLN 114 A CD GLN 115 1 Y 1 A OE1 GLN 114 A OE1 GLN 115 1 Y 1 A NE2 GLN 114 A NE2 GLN 115 1 Y 1 A CD2 TYR 123 A CD2 TYR 124 1 Y 1 A CE1 TYR 123 A CE1 TYR 124 1 Y 1 A CE2 TYR 123 A CE2 TYR 124 1 Y 1 A CZ TYR 123 A CZ TYR 124 1 Y 1 A OH TYR 123 A OH TYR 124 1 Y 1 A CG ASP 126 A CG ASP 127 1 Y 1 A OD1 ASP 126 A OD1 ASP 127 1 Y 1 A OD2 ASP 126 A OD2 ASP 127 1 Y 1 A CG ASN 127 A CG ASN 128 1 Y 1 A OD1 ASN 127 A OD1 ASN 128 1 Y 1 A ND2 ASN 127 A ND2 ASN 128 1 Y 1 A CD GLU 142 A CD GLU 143 1 Y 1 A OE1 GLU 142 A OE1 GLU 143 1 Y 1 A OE2 GLU 142 A OE2 GLU 143 1 Y 1 A CG GLU 148 A CG GLU 149 1 Y 1 A CD GLU 148 A CD GLU 149 1 Y 1 A OE1 GLU 148 A OE1 GLU 149 1 Y 1 A OE2 GLU 148 A OE2 GLU 149 1 Y 1 A CD GLU 155 A CD GLU 156 1 Y 1 A OE1 GLU 155 A OE1 GLU 156 1 Y 1 A OE2 GLU 155 A OE2 GLU 156 1 Y 1 A CD1 PHE 162 A CD1 PHE 163 1 Y 1 A CD2 PHE 162 A CD2 PHE 163 1 Y 1 A CE1 PHE 162 A CE1 PHE 163 1 Y 1 A CE2 PHE 162 A CE2 PHE 163 1 Y 1 A CZ PHE 162 A CZ PHE 163 1 Y 1 A CD LYS 167 A CD LYS 168 1 Y 1 A CE LYS 167 A CE LYS 168 1 Y 1 A NZ LYS 167 A NZ LYS 168 1 Y 1 A CD ARG 178 A CD ARG 179 1 Y 1 A NE ARG 178 A NE ARG 179 1 Y 1 A CZ ARG 178 A CZ ARG 179 1 Y 1 A NH1 ARG 178 A NH1 ARG 179 1 Y 1 A NH2 ARG 178 A NH2 ARG 179 1 Y 1 A CG ASP 185 A CG ASP 186 1 Y 1 A OD1 ASP 185 A OD1 ASP 186 1 Y 1 A OD2 ASP 185 A OD2 ASP 186 1 Y 1 A MET 0 A MET 1 1 Y 1 A HIS 1 A HIS 2 1 Y 1 A HIS 2 A HIS 3 1 Y 1 A HIS 3 A HIS 4 1 Y 1 A HIS 4 A HIS 5 1 Y 1 A HIS 5 A HIS 6 1 Y 1 A HIS 6 A HIS 7 1 Y 1 A SER 7 A SER 8 1 Y 1 A SER 8 A SER 9 1 Y 1 A GLY 9 A GLY 10 1 Y 1 A SER 188 A SER 189 1 Y 1 A ASP 189 A ASP 190 1 Y 1 A SER 190 A SER 191 1 Y 1 A SER 32 82.26 8.43 1 A ASP 58 -152.76 24.51 1 A LYS 136 74.96 31.26 1 A MET 139 -96.20 54.11 15.646 -1.208 0.000 -1.590 1.537 0.000 -1.464 0.947 0.915 ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY 0.251 0.211 0.213 1.900 20.000 763 15562 4.903 99.724 0.241 0.204 8.566 0.112 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.165 0.153 0.800 0.800 1.200 PDB ENTRY 2GF9 MAXIMUM LIKELIHOOD MASK BULK SOLVENT 1.900 20.000 30 1454 34 0 1390 0.014 0.022 1456 0.002 0.020 962 1.381 1.955 1976 0.862 3.000 2330 6.644 5.000 179 38.192 23.636 66 12.066 15.000 240 16.515 15.000 9 0.082 0.200 221 0.005 0.020 1618 0.001 0.020 324 1.403 2.000 884 0.415 2.000 364 2.134 3.000 1419 1.684 2.000 572 2.368 3.000 556 0.368 0.327 1.949 47 1037 1112 20 97.482 0.295 0.294 2.002 57 1053 1117 20 99.373 0.289 0.231 2.059 52 1003 1059 20 99.622 0.249 0.193 2.122 67 1020 1089 20 99.816 0.220 0.215 2.191 46 947 993 20 100.000 0.287 0.216 2.267 45 937 984 20 99.797 0.219 0.196 2.351 41 919 960 20 100.000 0.196 0.169 2.446 39 879 918 20 100.000 0.236 0.189 2.553 46 851 897 20 100.000 0.236 0.205 2.675 47 768 815 20 100.000 0.216 0.209 2.817 37 775 812 20 100.000 0.229 0.203 2.984 24 746 770 20 100.000 0.261 0.218 3.185 38 692 730 20 100.000 0.205 0.213 3.433 36 619 655 20 100.000 0.253 0.201 3.750 26 590 616 20 100.000 0.163 0.182 4.174 30 541 571 20 100.000 0.245 0.172 4.785 28 481 509 20 100.000 0.273 0.227 5.778 23 401 424 20 100.000 0.377 0.287 7.851 22 326 348 20 100.000 0.423 0.239 20.000 12 214 226 20 100.000 1.900 25.000 3DZ8 15627 0.061 1.518 1 6.700 99.700 0.609 1.90 1.97 1500 1.374 1 3.30 97.90 0.471 1.97 2.05 1569 1.403 1 5.00 99.60 0.370 2.05 2.14 1543 1.515 1 7.10 99.70 0.302 2.14 2.25 1563 1.488 1 7.20 100.00 0.218 2.25 2.39 1561 1.507 1 7.20 100.00 0.156 2.39 2.58 1555 1.532 1 7.30 100.00 0.108 2.58 2.84 1570 1.540 1 7.40 100.00 0.059 2.84 3.25 1570 1.497 1 7.50 100.00 0.033 3.25 4.09 1582 1.506 1 7.40 100.00 0.030 4.09 25.00 1614 1.676 1 7.40 100.00 data reduction Zbyszek Otwinowski zbyszek@mix.swmed.edu http://www.lnls.br/infra/linhasluz/denzo-hkl.htm DENZO package data scaling Zbyszek Otwinowski zbyszek@mix.swmed.edu http://www.lnls.br/infra/linhasluz/denzo-hkl.htm SCALEPACK package phasing R. J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER other refinement Murshudov, G.N. ccp4@dl.ac.uk Fortran_77 http://www.ccp4.ac.uk/main.html REFMAC program 5.5.0044 data extraction PDB sw-help@rcsb.rutgers.edu September 10, 2007 C++ http://pdb.rutgers.edu/software/ PDB_EXTRACT package 3.005 model building ARP/wARP model building Coot model building MolProbity Crystal structure of human Rab3B GTPase bound with GDP 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 4 N N A GLY 34 A GLY 35 HELX_P A THR 46 A THR 47 1 1 13 A ASP 77 A ASP 78 HELX_P A TYR 84 A TYR 85 1 2 8 A TYR 84 A TYR 85 HELX_P A ARG 93 A ARG 94 1 3 10 A ASN 106 A ASN 107 HELX_P A ALA 112 A ALA 113 1 4 7 A ALA 112 A ALA 113 HELX_P A SER 124 A SER 125 1 5 13 A MET 139 A MET 140 HELX_P A ARG 143 A ARG 144 5 6 5 A PRO 146 A PRO 147 HELX_P A GLY 158 A GLY 159 1 7 13 A SER 171 A SER 172 HELX_P A MET 187 A MET 188 1 8 17 PROTEIN TRANSPORT ras, gdp, gtpase, structural genomics consortium, sgc, Cell membrane, GTP-binding, Lipoprotein, Membrane, Methylation, Nucleotide-binding, Phosphoprotein, Prenylation, Protein transport, Transport RAB3B_HUMAN UNP 1 18 P20337 NFDYMFKLLIIGNSSVGKTSFLFRYADDTFTPAFVSTVGIDFKVKTVYRHEKRVKLQIWDTAGQERYRTITTAYYRGAMG FILMYDITNEESFNAVQDWATQIKTYSWDNAQVILVGNKCDMEEERVVPTEKGQLLAEQLGFDFFEASAKENISVRQAFE RLVDAICDKMSDS 18 190 3DZ8 18 190 P20337 A 1 19 191 1 expression tag MET 0 3DZ8 A P20337 UNP 1 1 expression tag HIS 1 3DZ8 A P20337 UNP 2 1 expression tag HIS 2 3DZ8 A P20337 UNP 3 1 expression tag HIS 3 3DZ8 A P20337 UNP 4 1 expression tag HIS 4 3DZ8 A P20337 UNP 5 1 expression tag HIS 5 3DZ8 A P20337 UNP 6 1 expression tag HIS 6 3DZ8 A P20337 UNP 7 1 expression tag SER 7 3DZ8 A P20337 UNP 8 1 expression tag SER 8 3DZ8 A P20337 UNP 9 1 expression tag GLY 9 3DZ8 A P20337 UNP 10 1 expression tag ARG 10 3DZ8 A P20337 UNP 11 1 expression tag GLU 11 3DZ8 A P20337 UNP 12 1 expression tag ASN 12 3DZ8 A P20337 UNP 13 1 expression tag LEU 13 3DZ8 A P20337 UNP 14 1 expression tag TYR 14 3DZ8 A P20337 UNP 15 1 expression tag PHE 15 3DZ8 A P20337 UNP 16 1 expression tag GLN 16 3DZ8 A P20337 UNP 17 1 expression tag GLY 17 3DZ8 A P20337 UNP 18 2 7 anti-parallel anti-parallel anti-parallel parallel parallel parallel parallel A ASN 12 A ASN 13 A PHE 15 A PHE 16 A ASN 18 A ASN 19 A TYR 21 A TYR 22 A PHE 51 A PHE 52 A VAL 55 A VAL 56 A PHE 59 A PHE 60 A ARG 66 A ARG 67 A VAL 71 A VAL 72 A TRP 76 A TRP 77 A PHE 23 A PHE 24 A GLY 29 A GLY 30 A GLY 97 A GLY 98 A ASP 103 A ASP 104 A GLN 129 A GLN 130 A ASN 135 A ASN 136 A ASP 160 A ASP 161 A GLU 163 A GLU 164 BINDING SITE FOR RESIDUE GDP A 201 A GDP 201 Software 15 BINDING SITE FOR RESIDUE UNX A 501 A UNX 501 Software 3 BINDING SITE FOR RESIDUE UNX A 502 A UNX 502 Software 5 BINDING SITE FOR RESIDUE UNX A 504 A UNX 504 Software 2 BINDING SITE FOR RESIDUE UNX A 505 A UNX 505 Software 2 A SER 32 A SER 33 15 1_555 A GLY 34 A GLY 35 15 1_555 A LYS 35 A LYS 36 15 1_555 A THR 36 A THR 37 15 1_555 A SER 37 A SER 38 15 1_555 A ASN 135 A ASN 136 15 1_555 A LYS 136 A LYS 137 15 1_555 A ASP 138 A ASP 139 15 1_555 A MET 139 A MET 140 15 1_555 A SER 165 A SER 166 15 1_555 A ALA 166 A ALA 167 15 1_555 A LYS 167 A LYS 168 15 1_555 A HOH 511 I HOH 15 1_555 A HOH 520 I HOH 15 1_555 A HOH 522 I HOH 15 1_555 A SER 31 A SER 32 3 1_555 A ALA 79 A ALA 80 3 1_555 A HOH 510 I HOH 3 1_555 A PHE 15 A PHE 16 5 2_656 A GLN 16 A GLN 17 5 2_656 A ALA 43 A ALA 44 5 1_555 A ASP 44 A ASP 45 5 1_555 A THR 48 A THR 49 5 1_555 A ARG 66 A ARG 67 2 1_555 A ARG 173 A ARG 174 2 1_555 A ASN 169 A ASN 170 2 1_555 A ARG 173 A ARG 174 2 1_555 5 C 1 2 1