0.005445 0.003144 0.000000 -0.000000 0.006288 0.000000 0.000000 -0.000000 0.022119 0.000000 0.000000 0.000000 Usha, V. Dover, L.G. Roper, D.I. Futterer, K. Besra, G.S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.000 90.000 120.000 183.640 183.640 45.210 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 C4 H10 O2 S2 154.251 2,3-DIHYDROXY-1,4-DITHIOBUTANE 1,4-DITHIOTHREITOL non-polymer 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 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 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 S N 89 N C N 90 R C N 91 N O N 92 R C N 93 N O N 94 N C N 95 N S N 96 N H N 97 N H N 98 N H N 99 N H N 100 N H N 101 N H N 102 N H N 103 N H N 104 N H N 105 N H N 106 N N N 107 S C N 108 N C N 109 N O N 110 N C N 111 N C N 112 N C N 113 N O N 114 N N N 115 N O 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 N N 127 S C N 128 N C N 129 N O N 130 N C N 131 N C N 132 N C N 133 N O N 134 N O N 135 N O N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 143 N H N 144 N H N 145 N N N 146 N C N 147 N C N 148 N O N 149 N O N 150 N H N 151 N H N 152 N H N 153 N H N 154 N H N 155 N C N 156 N O N 157 N C N 158 N O N 159 N C 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 N N 170 S C N 171 N C N 172 N O N 173 N C Y 174 N C Y 175 N N Y 176 N C Y 177 N C Y 178 N N N 179 N O N 180 N H N 181 N H N 182 N H N 183 N H N 184 N H N 185 N H N 186 N H N 187 N H N 188 N H N 189 N H N 190 N O N 191 N H N 192 N H N 193 N N N 194 S C N 195 N C N 196 N O N 197 S C N 198 N C N 199 N C N 200 N C N 201 N O N 202 N H N 203 N H N 204 N H N 205 N H N 206 N H N 207 N H N 208 N H N 209 N H N 210 N H N 211 N H N 212 N H N 213 N H N 214 N H N 215 N N N 216 S C N 217 N C N 218 N O N 219 N C N 220 N C N 221 N C N 222 N C N 223 N O N 224 N H N 225 N H N 226 N H N 227 N H N 228 N H N 229 N H N 230 N H N 231 N H N 232 N H N 233 N H N 234 N H N 235 N H N 236 N H N 237 N N N 238 S C N 239 N C N 240 N O N 241 N C N 242 N C N 243 N C N 244 N C N 245 N N N 246 N O N 247 N H N 248 N H N 249 N H N 250 N H N 251 N H N 252 N H N 253 N H N 254 N H N 255 N H N 256 N H N 257 N H N 258 N H N 259 N H N 260 N H N 261 N H N 262 N N N 263 S C N 264 N C N 265 N O N 266 N C N 267 N C N 268 N S N 269 N C N 270 N O N 271 N H N 272 N H N 273 N H N 274 N H N 275 N H N 276 N H N 277 N H N 278 N H N 279 N H N 280 N H N 281 N H N 282 N N N 283 S C N 284 N C N 285 N O N 286 N C Y 287 N C Y 288 N C Y 289 N C Y 290 N C Y 291 N C Y 292 N C N 293 N O N 294 N H N 295 N H N 296 N H N 297 N H N 298 N H N 299 N H N 300 N H N 301 N H N 302 N H N 303 N H N 304 N H N 305 N N N 306 S C N 307 N C N 308 N O N 309 N C N 310 N C N 311 N C N 312 N O N 313 N H N 314 N H N 315 N H N 316 N H N 317 N H N 318 N H N 319 N H N 320 N H N 321 N H N 322 N N N 323 S C N 324 N C N 325 N O N 326 N C N 327 N O N 328 N O N 329 N H N 330 N H N 331 N H N 332 N H N 333 N H N 334 N H N 335 N H N 336 N N N 337 S C N 338 N C N 339 N O N 340 R C N 341 N O N 342 N C N 343 N O N 344 N H N 345 N H N 346 N H N 347 N H N 348 N H N 349 N H N 350 N H N 351 N H N 352 N H N 353 N N N 354 S C N 355 N C N 356 N O N 357 N C Y 358 N C Y 359 N C Y 360 N C Y 361 N N Y 362 N C Y 363 N C Y 364 N C Y 365 N C Y 366 N C N 367 N O N 368 N H N 369 N H N 370 N H N 371 N H N 372 N H N 373 N H N 374 N H N 375 N H N 376 N H N 377 N H N 378 N H N 379 N H N 380 N N N 381 S C N 382 N C N 383 N O N 384 N C Y 385 N C Y 386 N C Y 387 N C Y 388 N C Y 389 N C Y 390 N C N 391 N O N 392 N O N 393 N H N 394 N H N 395 N H N 396 N H N 397 N H N 398 N H N 399 N H N 400 N H N 401 N H N 402 N H N 403 N H N 404 N N N 405 S C N 406 N C N 407 N O N 408 N C N 409 N C N 410 N C N 411 N O N 412 N H N 413 N H N 414 N H N 415 N H N 416 N H N 417 N H N 418 N H N 419 N H N 420 N H N 421 N H N 422 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 sing 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 sing 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 doub N 107 N sing N 108 N sing N 109 N sing N 110 N sing N 111 N sing N 112 N sing N 113 N sing N 114 N doub N 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N doub 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 doub N 134 N sing 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 sing N 143 N doub 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 sing 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 sing N 162 N sing N 163 N sing N 164 N sing N 165 N doub N 166 N sing N 167 N sing N 168 N sing N 169 N sing Y 170 N sing Y 171 N doub Y 172 N doub N 173 N sing Y 174 N sing N 175 N sing Y 176 N sing N 177 N sing N 178 N sing N 179 N sing N 180 N sing N 181 N sing N 182 N sing N 183 N sing N 184 N sing N 185 N sing N 186 N sing N 187 N sing N 188 N doub N 189 N sing N 190 N sing N 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 sing N 204 N sing N 205 N sing N 206 N sing N 207 N sing N 208 N sing N 209 N doub 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 sing N 225 N sing N 226 N sing N 227 N sing N 228 N sing N 229 N sing N 230 N doub 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 sing 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 doub 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 sing N 270 N sing N 271 N sing N 272 N sing N 273 N doub N 274 N sing N 275 N sing N 276 N sing N 277 N sing Y 278 N doub Y 279 N sing Y 280 N sing N 281 N sing Y 282 N doub N 283 N sing Y 284 N doub N 285 N sing Y 286 N sing N 287 N sing N 288 N sing N 289 N sing N 290 N sing N 291 N sing N 292 N sing N 293 N sing N 294 N sing N 295 N sing N 296 N doub N 297 N sing N 298 N sing N 299 N sing N 300 N sing N 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 sing N 312 N sing N 313 N doub 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 doub N 327 N sing N 328 N sing 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 sing N 342 N doub N 343 N sing N 344 N sing N 345 N sing N 346 N sing Y 347 N doub Y 348 N sing Y 349 N sing N 350 N sing Y 351 N doub Y 352 N sing Y 353 N sing N 354 N sing Y 355 N sing Y 356 N doub N 357 N sing Y 358 N doub N 359 N sing Y 360 N sing N 361 N sing N 362 N sing N 363 N sing N 364 N sing N 365 N sing N 366 N sing N 367 N sing N 368 N sing N 369 N sing N 370 N doub N 371 N sing N 372 N sing N 373 N sing N 374 N sing Y 375 N doub Y 376 N sing Y 377 N sing N 378 N sing Y 379 N doub N 380 N sing Y 381 N doub N 382 N sing Y 383 N sing N 384 N sing N 385 N sing N 386 N sing N 387 N sing N 388 N sing N 389 N sing N 390 N sing N 391 N sing N 392 N sing N 393 N sing N 394 N doub N 395 N sing N 396 N sing N 397 N sing N 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 DK Acta Crystallogr.,Sect.D ABCRE6 0766 0907-4449 65 383 387 10.1107/S0907444909002522 19307721 Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis 2009 10.2210/pdb3fve/pdb pdb_00003fve 100 1 CCD 2008-09-27 ADSC QUANTUM Q315r Double crystal, Si(111) or Si(311) SINGLE WAVELENGTH M x-ray 1 0.976 1.0 ID29 ESRF 0.976 SYNCHROTRON ESRF BEAMLINE ID29 29864.635 Diaminopimelate epimerase 5.1.1.7 1 man polymer 154.251 2,3-DIHYDROXY-1,4-DITHIOBUTANE 1 syn non-polymer 92.094 GLYCEROL 2 syn non-polymer 18.015 water 38 nat water DAP epimerase no no HMIFAKGHGTQNDFVLLPDVDAELVLTAARVAALCDRRKGLGADGVLRVTTAGAAQAVGVLDSLPEGVRVTDWYMDYRNA DGSAAQMCGNGVRVFAHYLRASGLEVRDEFVVGSLAGPRPVTCHHVEAAYADVSVDMGKANRLGAGEAVVGGRRFHGLAV DVGNPHLACVDSQLTVDGLAALDVGAPVSFDGAQFPDGVNVEVLTAPVDGAVWMRVHERGVGETRSCGTGTVAAAVAALA AVGSPTGTLTVHVPGGEVVVTVTDATSFLRGPSVLVARGDLADDWWNAMG HMIFAKGHGTQNDFVLLPDVDAELVLTAARVAALCDRRKGLGADGVLRVTTAGAAQAVGVLDSLPEGVRVTDWYMDYRNA DGSAAQMCGNGVRVFAHYLRASGLEVRDEFVVGSLAGPRPVTCHHVEAAYADVSVDMGKANRLGAGEAVVGGRRFHGLAV DVGNPHLACVDSQLTVDGLAALDVGAPVSFDGAQFPDGVNVEVLTAPVDGAVWMRVHERGVGETRSCGTGTVAAAVAALA AVGSPTGTLTVHVPGGEVVVTVTDATSFLRGPSVLVARGDLADDWWNAMG 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n H37RV sample dapF, MT2798, MTCY154.06c, Rv2726c 1773 Mycobacterium tuberculosis 562 Escherichia coli C41(DE3) plasmid pET28a 1 3.68 66.62 VAPOR DIFFUSION 9.5 1.9 M (NH4)H2PO4, 0.1 M bis-tris propane, pH 9.5, 2.5% glycerol, vapor diffusion, temperature 291K, VAPOR DIFFUSION 291 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 Data collection Database references Derived calculations Refinement description 1 0 2009-01-27 1 1 2011-07-13 1 2 2023-09-06 _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 RCSB Y RCSB 2009-01-15 REL REL DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE GOL GLYCEROL HOH water 1BWZ PDB entry 1BWZ PDB experimental model DTT 1 2 DTT DTT 290 A GOL 2 3 GOL GOL 291 A GOL 3 3 GOL GOL 292 A HOH 2 4 HOH HOH 293 A HOH 3 4 HOH HOH 294 A HOH 4 4 HOH HOH 295 A HOH 5 4 HOH HOH 296 A HOH 6 4 HOH HOH 297 A HOH 7 4 HOH HOH 298 A HOH 9 4 HOH HOH 299 A HOH 10 4 HOH HOH 300 A HOH 11 4 HOH HOH 301 A HOH 12 4 HOH HOH 302 A HOH 13 4 HOH HOH 303 A HOH 14 4 HOH HOH 304 A HOH 15 4 HOH HOH 305 A HOH 16 4 HOH HOH 306 A HOH 17 4 HOH HOH 307 A HOH 18 4 HOH HOH 308 A HOH 19 4 HOH HOH 309 A HOH 20 4 HOH HOH 310 A HOH 21 4 HOH HOH 311 A HOH 22 4 HOH HOH 312 A HOH 24 4 HOH HOH 313 A HOH 25 4 HOH HOH 314 A HOH 26 4 HOH HOH 315 A HOH 27 4 HOH HOH 316 A HOH 28 4 HOH HOH 317 A HOH 29 4 HOH HOH 318 A HOH 31 4 HOH HOH 319 A HOH 33 4 HOH HOH 320 A HOH 34 4 HOH HOH 321 A HOH 35 4 HOH HOH 322 A HOH 36 4 HOH HOH 323 A HOH 37 4 HOH HOH 324 A HOH 38 4 HOH HOH 325 A HOH 39 4 HOH HOH 326 A HOH 40 4 HOH HOH 327 A HOH 41 4 HOH HOH 328 A HOH 43 4 HOH HOH 329 A HOH 44 4 HOH HOH 330 A 3.500 3.500 9.990 9.990 Phaser MODE: MR_AUTO HIS 0 n 1 HIS 0 A MET 1 n 2 MET 1 A ILE 2 n 3 ILE 2 A PHE 3 n 4 PHE 3 A ALA 4 n 5 ALA 4 A LYS 5 n 6 LYS 5 A GLY 6 n 7 GLY 6 A HIS 7 n 8 HIS 7 A GLY 8 n 9 GLY 8 A THR 9 n 10 THR 9 A GLN 10 n 11 GLN 10 A ASN 11 n 12 ASN 11 A ASP 12 n 13 ASP 12 A PHE 13 n 14 PHE 13 A VAL 14 n 15 VAL 14 A LEU 15 n 16 LEU 15 A LEU 16 n 17 LEU 16 A PRO 17 n 18 PRO 17 A ASP 18 n 19 ASP 18 A VAL 19 n 20 VAL 19 A ASP 20 n 21 ASP 20 A ALA 21 n 22 ALA 21 A GLU 22 n 23 GLU 22 A LEU 23 n 24 LEU 23 A VAL 24 n 25 VAL 24 A LEU 25 n 26 LEU 25 A THR 26 n 27 THR 26 A ALA 27 n 28 ALA 27 A ALA 28 n 29 ALA 28 A ARG 29 n 30 ARG 29 A VAL 30 n 31 VAL 30 A ALA 31 n 32 ALA 31 A ALA 32 n 33 ALA 32 A LEU 33 n 34 LEU 33 A CYS 34 n 35 CYS 34 A ASP 35 n 36 ASP 35 A ARG 36 n 37 ARG 36 A ARG 37 n 38 ARG 37 A LYS 38 n 39 LYS 38 A GLY 39 n 40 GLY 39 A LEU 40 n 41 LEU 40 A GLY 41 n 42 GLY 41 A ALA 42 n 43 ALA 42 A ASP 43 n 44 ASP 43 A GLY 44 n 45 GLY 44 A VAL 45 n 46 VAL 45 A LEU 46 n 47 LEU 46 A ARG 47 n 48 ARG 47 A VAL 48 n 49 VAL 48 A THR 49 n 50 THR 49 A THR 50 n 51 THR 50 A ALA 51 n 52 ALA 51 A GLY 52 n 53 GLY 52 A ALA 53 n 54 ALA 53 A ALA 54 n 55 ALA 54 A GLN 55 n 56 GLN 55 A ALA 56 n 57 ALA 56 A VAL 57 n 58 VAL 57 A GLY 58 n 59 GLY 58 A VAL 59 n 60 VAL 59 A LEU 60 n 61 LEU 60 A ASP 61 n 62 ASP 61 A SER 62 n 63 SER 62 A LEU 63 n 64 LEU 63 A PRO 64 n 65 PRO 64 A GLU 65 n 66 GLU 65 A GLY 66 n 67 GLY 66 A VAL 67 n 68 VAL 67 A ARG 68 n 69 ARG 68 A VAL 69 n 70 VAL 69 A THR 70 n 71 THR 70 A ASP 71 n 72 ASP 71 A TRP 72 n 73 TRP 72 A TYR 73 n 74 TYR 73 A MET 74 n 75 MET 74 A ASP 75 n 76 ASP 75 A TYR 76 n 77 TYR 76 A ARG 77 n 78 ARG 77 A ASN 78 n 79 ASN 78 A ALA 79 n 80 ALA 79 A ASP 80 n 81 ASP 80 A GLY 81 n 82 GLY 81 A SER 82 n 83 SER 82 A ALA 83 n 84 ALA 83 A ALA 84 n 85 ALA 84 A GLN 85 n 86 GLN 85 A MET 86 n 87 MET 86 A CYS 87 n 88 CYS 87 A GLY 88 n 89 GLY 88 A ASN 89 n 90 ASN 89 A GLY 90 n 91 GLY 90 A VAL 91 n 92 VAL 91 A ARG 92 n 93 ARG 92 A VAL 93 n 94 VAL 93 A PHE 94 n 95 PHE 94 A ALA 95 n 96 ALA 95 A HIS 96 n 97 HIS 96 A TYR 97 n 98 TYR 97 A LEU 98 n 99 LEU 98 A ARG 99 n 100 ARG 99 A ALA 100 n 101 ALA 100 A SER 101 n 102 SER 101 A GLY 102 n 103 GLY 102 A LEU 103 n 104 LEU 103 A GLU 104 n 105 GLU 104 A VAL 105 n 106 VAL 105 A ARG 106 n 107 ARG 106 A ASP 107 n 108 ASP 107 A GLU 108 n 109 GLU 108 A PHE 109 n 110 PHE 109 A VAL 110 n 111 VAL 110 A VAL 111 n 112 VAL 111 A GLY 112 n 113 GLY 112 A SER 113 n 114 SER 113 A LEU 114 n 115 LEU 114 A ALA 115 n 116 ALA 115 A GLY 116 n 117 GLY 116 A PRO 117 n 118 PRO 117 A ARG 118 n 119 ARG 118 A PRO 119 n 120 PRO 119 A VAL 120 n 121 VAL 120 A THR 121 n 122 THR 121 A CYS 122 n 123 CYS 122 A HIS 123 n 124 HIS 123 A HIS 124 n 125 HIS 124 A VAL 125 n 126 VAL 125 A GLU 126 n 127 GLU 126 A ALA 127 n 128 ALA 127 A ALA 128 n 129 ALA 128 A TYR 129 n 130 TYR 129 A ALA 130 n 131 ALA 130 A ASP 131 n 132 ASP 131 A VAL 132 n 133 VAL 132 A SER 133 n 134 SER 133 A VAL 134 n 135 VAL 134 A ASP 135 n 136 ASP 135 A MET 136 n 137 MET 136 A GLY 137 n 138 GLY 137 A LYS 138 n 139 LYS 138 A ALA 139 n 140 ALA 139 A ASN 140 n 141 ASN 140 A ARG 141 n 142 ARG 141 A LEU 142 n 143 LEU 142 A GLY 143 n 144 GLY 143 A ALA 144 n 145 ALA 144 A GLY 145 n 146 GLY 145 A GLU 146 n 147 GLU 146 A ALA 147 n 148 ALA 147 A VAL 148 n 149 VAL 148 A n 150 149 A n 151 150 A n 152 151 A n 153 152 A n 154 153 A PHE 154 n 155 PHE 154 A HIS 155 n 156 HIS 155 A GLY 156 n 157 GLY 156 A LEU 157 n 158 LEU 157 A ALA 158 n 159 ALA 158 A VAL 159 n 160 VAL 159 A ASP 160 n 161 ASP 160 A VAL 161 n 162 VAL 161 A GLY 162 n 163 GLY 162 A ASN 163 n 164 ASN 163 A PRO 164 n 165 PRO 164 A HIS 165 n 166 HIS 165 A LEU 166 n 167 LEU 166 A ALA 167 n 168 ALA 167 A CYS 168 n 169 CYS 168 A VAL 169 n 170 VAL 169 A ASP 170 n 171 ASP 170 A SER 171 n 172 SER 171 A GLN 172 n 173 GLN 172 A LEU 173 n 174 LEU 173 A THR 174 n 175 THR 174 A VAL 175 n 176 VAL 175 A ASP 176 n 177 ASP 176 A GLY 177 n 178 GLY 177 A LEU 178 n 179 LEU 178 A ALA 179 n 180 ALA 179 A ALA 180 n 181 ALA 180 A LEU 181 n 182 LEU 181 A ASP 182 n 183 ASP 182 A VAL 183 n 184 VAL 183 A GLY 184 n 185 GLY 184 A n 186 185 A n 187 186 A VAL 187 n 188 VAL 187 A SER 188 n 189 SER 188 A PHE 189 n 190 PHE 189 A ASP 190 n 191 ASP 190 A GLY 191 n 192 GLY 191 A ALA 192 n 193 ALA 192 A GLN 193 n 194 GLN 193 A PHE 194 n 195 PHE 194 A PRO 195 n 196 PRO 195 A ASP 196 n 197 ASP 196 A GLY 197 n 198 GLY 197 A VAL 198 n 199 VAL 198 A ASN 199 n 200 ASN 199 A VAL 200 n 201 VAL 200 A GLU 201 n 202 GLU 201 A VAL 202 n 203 VAL 202 A LEU 203 n 204 LEU 203 A THR 204 n 205 THR 204 A ALA 205 n 206 ALA 205 A PRO 206 n 207 PRO 206 A VAL 207 n 208 VAL 207 A ASP 208 n 209 ASP 208 A GLY 209 n 210 GLY 209 A ALA 210 n 211 ALA 210 A VAL 211 n 212 VAL 211 A TRP 212 n 213 TRP 212 A MET 213 n 214 MET 213 A ARG 214 n 215 ARG 214 A VAL 215 n 216 VAL 215 A HIS 216 n 217 HIS 216 A GLU 217 n 218 GLU 217 A ARG 218 n 219 ARG 218 A GLY 219 n 220 GLY 219 A VAL 220 n 221 VAL 220 A GLY 221 n 222 GLY 221 A GLU 222 n 223 GLU 222 A THR 223 n 224 THR 223 A ARG 224 n 225 ARG 224 A SER 225 n 226 SER 225 A CYS 226 n 227 CYS 226 A GLY 227 n 228 GLY 227 A THR 228 n 229 THR 228 A GLY 229 n 230 GLY 229 A THR 230 n 231 THR 230 A VAL 231 n 232 VAL 231 A ALA 232 n 233 ALA 232 A ALA 233 n 234 ALA 233 A ALA 234 n 235 ALA 234 A VAL 235 n 236 VAL 235 A ALA 236 n 237 ALA 236 A ALA 237 n 238 ALA 237 A LEU 238 n 239 LEU 238 A ALA 239 n 240 ALA 239 A ALA 240 n 241 ALA 240 A VAL 241 n 242 VAL 241 A GLY 242 n 243 GLY 242 A SER 243 n 244 SER 243 A PRO 244 n 245 PRO 244 A THR 245 n 246 THR 245 A GLY 246 n 247 GLY 246 A THR 247 n 248 THR 247 A LEU 248 n 249 LEU 248 A THR 249 n 250 THR 249 A VAL 250 n 251 VAL 250 A HIS 251 n 252 HIS 251 A VAL 252 n 253 VAL 252 A PRO 253 n 254 PRO 253 A GLY 254 n 255 GLY 254 A GLY 255 n 256 GLY 255 A GLU 256 n 257 GLU 256 A VAL 257 n 258 VAL 257 A VAL 258 n 259 VAL 258 A VAL 259 n 260 VAL 259 A THR 260 n 261 THR 260 A VAL 261 n 262 VAL 261 A THR 262 n 263 THR 262 A ASP 263 n 264 ASP 263 A ALA 264 n 265 ALA 264 A THR 265 n 266 THR 265 A SER 266 n 267 SER 266 A PHE 267 n 268 PHE 267 A LEU 268 n 269 LEU 268 A ARG 269 n 270 ARG 269 A GLY 270 n 271 GLY 270 A PRO 271 n 272 PRO 271 A SER 272 n 273 SER 272 A VAL 273 n 274 VAL 273 A LEU 274 n 275 LEU 274 A VAL 275 n 276 VAL 275 A ALA 276 n 277 ALA 276 A ARG 277 n 278 ARG 277 A GLY 278 n 279 GLY 278 A ASP 279 n 280 ASP 279 A LEU 280 n 281 LEU 280 A ALA 281 n 282 ALA 281 A ASP 282 n 283 ASP 282 A ASP 283 n 284 ASP 283 A TRP 284 n 285 TRP 284 A TRP 285 n 286 TRP 285 A ASN 286 n 287 ASN 286 A ALA 287 n 288 ALA 287 A MET 288 n 289 MET 288 A GLY 289 n 290 GLY 289 A 4.0218 0.6657 -1.4457 1.8749 -1.1234 1.7028 -0.2642 -0.0106 -0.8263 -0.2333 -0.0463 -0.1792 0.3722 0.0664 0.3105 0.0183 -0.0220 0.0786 0.0388 -0.0327 0.1083 refined -17.3890 73.2990 -3.4700 X-RAY DIFFRACTION A 1 A 300 X-RAY DIFFRACTION 1 author_defined_assembly 1 monomeric author_and_software_defined_assembly PISA 2 dimeric 3400 -11 22510 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 11_554 -x+y,y,-z-1/2 crystal symmetry operation 0.0000000000 0.0000000000 -22.6050000000 A N LEU 142 A N LEU 143 A O ALA 158 A O ALA 159 A N LEU 157 A N LEU 158 A O ALA 167 A O ALA 168 A N CYS 168 A N CYS 169 A O LEU 203 A O LEU 204 A N THR 204 A N THR 205 A O TRP 212 A O TRP 213 A N VAL 211 A N VAL 212 A O HIS 251 A O HIS 252 A N VAL 250 A N VAL 251 A O VAL 257 A O VAL 258 A N THR 260 A N THR 261 A O PHE 267 A O PHE 268 A O LEU 268 A O LEU 269 A N VAL 134 A N VAL 135 A O ASP 135 A O ASP 136 A N PRO 119 A N PRO 120 A O VAL 120 A O VAL 121 A N PHE 109 A N PHE 110 A O GLY 112 A O GLY 113 A N MET 74 A N MET 75 A O TYR 73 A O TYR 74 A N THR 49 A N THR 50 A O LEU 46 A O LEU 47 A N VAL 14 A N VAL 15 A O PHE 13 A O PHE 14 A N GLY 6 A N GLY 7 A N MET 1 A N MET 2 A O LEU 280 A O LEU 281 1 A CG HIS 0 A CG HIS 1 1 Y 1 A ND1 HIS 0 A ND1 HIS 1 1 Y 1 A CD2 HIS 0 A CD2 HIS 1 1 Y 1 A CE1 HIS 0 A CE1 HIS 1 1 Y 1 A NE2 HIS 0 A NE2 HIS 1 1 Y 1 A CG ASP 61 A CG ASP 62 1 Y 1 A OD1 ASP 61 A OD1 ASP 62 1 Y 1 A OD2 ASP 61 A OD2 ASP 62 1 Y 1 A CG GLU 65 A CG GLU 66 1 Y 1 A CD GLU 65 A CD GLU 66 1 Y 1 A OE1 GLU 65 A OE1 GLU 66 1 Y 1 A OE2 GLU 65 A OE2 GLU 66 1 Y 1 A CG GLN 85 A CG GLN 86 1 Y 1 A CD GLN 85 A CD GLN 86 1 Y 1 A OE1 GLN 85 A OE1 GLN 86 1 Y 1 A NE2 GLN 85 A NE2 GLN 86 1 Y 1 A CD1 LEU 142 A CD1 LEU 143 1 Y 1 A CD2 LEU 142 A CD2 LEU 143 1 Y 1 A CG GLU 146 A CG GLU 147 1 Y 1 A CD GLU 146 A CD GLU 147 1 Y 1 A OE1 GLU 146 A OE1 GLU 147 1 Y 1 A OE2 GLU 146 A OE2 GLU 147 1 Y 1 A CG LEU 181 A CG LEU 182 1 Y 1 A CD1 LEU 181 A CD1 LEU 182 1 Y 1 A CD2 LEU 181 A CD2 LEU 182 1 Y 1 A CG1 VAL 183 A CG1 VAL 184 1 Y 1 A CG2 VAL 183 A CG2 VAL 184 1 Y 1 A CG1 VAL 187 A CG1 VAL 188 1 Y 1 A CG2 VAL 187 A CG2 VAL 188 1 Y 1 A CG ASP 208 A CG ASP 209 1 Y 1 A OD1 ASP 208 A OD1 ASP 209 1 Y 1 A OD2 ASP 208 A OD2 ASP 209 1 Y 1 A OG1 THR 223 A OG1 THR 224 1 Y 1 A CG2 THR 223 A CG2 THR 224 1 Y 1 A CG ARG 224 A CG ARG 225 1 Y 1 A CD ARG 224 A CD ARG 225 1 Y 1 A NE ARG 224 A NE ARG 225 1 Y 1 A CZ ARG 224 A CZ ARG 225 1 Y 1 A NH1 ARG 224 A NH1 ARG 225 1 Y 1 A NH2 ARG 224 A NH2 ARG 225 1 Y 1 A CG2 THR 228 A CG2 THR 229 1 Y 1 A CG1 VAL 241 A CG1 VAL 242 1 Y 1 A CG2 VAL 241 A CG2 VAL 242 1 Y 1 A VAL 149 A VAL 150 1 Y 1 A GLY 150 A GLY 151 1 Y 1 A GLY 151 A GLY 152 1 Y 1 A ARG 152 A ARG 153 1 Y 1 A ARG 153 A ARG 154 1 Y 1 A ALA 185 A ALA 186 1 Y 1 A PRO 186 A PRO 187 1 Y 1 A C3 DTT 290 WRONG HAND 1 A A CG OD1 ASP ASP 176 176 0.162 0.023 1.249 1.411 N 1 A GLN 10 -139.68 -56.43 1 A ASP 18 -162.35 68.35 1 A ASP 61 -84.43 -78.36 1 A ASP 80 -84.53 36.76 1 A ALA 84 -14.33 82.67 1 A GLN 85 -49.56 156.27 1 A CYS 87 -37.84 -32.11 1 A LEU 142 -140.18 47.83 1 A PRO 206 -57.84 109.95 1 A ARG 224 41.11 -130.00 83.85 38.103 27.12 -1.060 -0.530 -0.000 -1.060 0.000 1.580 0.931 0.908 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.254 0.224 0.226 0.226 2.600 45.000 722 14341 14341 5.000 99.970 0.244 0.229 1.00 1.00 0.807 20.884 0.213 0.416 0.291 RANDOM LIKELY RESIDUAL 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT 0.367 0.262 0.800 0.800 1.200 PDB entry 1BWZ MAXIMUM LIKELIHOOD MASK 2.600 45.000 38 2061 20 0 2003 0.009 0.021 2055 1.362 1.945 2799 5.639 5.000 280 34.896 23.165 79 18.300 15.000 270 17.410 15.000 15 0.070 0.200 329 0.003 0.020 1571 0.211 0.200 820 0.305 0.200 1363 0.123 0.200 73 0.152 0.200 33 0.121 0.200 6 0.458 1.500 1407 0.817 2.000 2184 0.966 3.000 718 1.609 4.500 615 0.456 0.341 2.668 45 994 1039 20 99.810 64.8 2.59 45.22 3FVE 14430 14430 0 0 0.086 0.086 1 13.2 99.7 0.758 2.59 2.73 3.8 2020 0.758 1 13.0 98.4 phasing Randy J. Read cimr-phaser@lists.cam.ac.uk http://www-structmed.cimr.cam.ac.uk/phaser/ PHASER program refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 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 collection ADSC Quantum data reduction XDS data scaling SCALA Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF 1 N N 2 N N 3 N N 3 N N 4 N N BIOLOGICAL UNIT IS THE SAME AS ASYM. A THR 26 A THR 27 HELX_P A ASP 35 A ASP 36 1 1 10 A ALA 51 A ALA 52 HELX_P A VAL 57 A VAL 58 1 2 7 A GLY 90 A GLY 91 HELX_P A SER 101 A SER 102 1 3 12 A CYS 226 A CYS 227 HELX_P A VAL 241 A VAL 242 1 4 16 A ALA 281 A ALA 282 HELX_P A ALA 287 A ALA 288 1 5 7 ISOMERASE alpha/beta, Amino-acid biosynthesis, Isomerase, Lysine biosynthesis DAPF_MYCTU UNP 1 1 P63897 MIFAKGHGTQNDFVLLPDVDAELVLTAARVAALCDRRKGLGADGVLRVTTAGAAQAVGVLDSLPEGVRVTDWYMDYRNAD GSAAQMCGNGVRVFAHYLRASGLEVRDEFVVGSLAGPRPVTCHHVEAAYADVSVDMGKANRLGAGEAVVGGRRFHGLAVD VGNPHLACVDSQLTVDGLAALDVGAPVSFDGAQFPDGVNVEVLTAPVDGAVWMRVHERGVGETRSCGTGTVAAAVAALAA VGSPTGTLTVHVPGGEVVVTVTDATSFLRGPSVLVARGDLADDWWNAMG 1 289 3FVE 1 289 P63897 A 1 2 290 1 expression tag HIS 0 3FVE A P63897 UNP 1 16 anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel parallel anti-parallel parallel anti-parallel anti-parallel A ASN 140 A ASN 141 A GLU 146 A GLU 147 A HIS 155 A HIS 156 A ASP 160 A ASP 161 A PRO 164 A PRO 165 A ASP 170 A ASP 171 A ASN 199 A ASN 200 A THR 204 A THR 205 A ALA 210 A ALA 211 A HIS 216 A HIS 217 A GLY 246 A GLY 247 A VAL 252 A VAL 253 A GLY 255 A GLY 256 A VAL 261 A VAL 262 A SER 266 A SER 267 A LEU 280 A LEU 281 A TYR 129 A TYR 130 A ASP 135 A ASP 136 A ARG 118 A ARG 119 A VAL 125 A VAL 126 A GLU 108 A GLU 109 A GLY 112 A GLY 113 A TRP 72 A TRP 73 A ASN 78 A ASN 79 A GLY 44 A GLY 45 A THR 50 A THR 51 A ASP 12 A ASP 13 A PRO 17 A PRO 18 A MET 1 A MET 2 A HIS 7 A HIS 8 A SER 266 A SER 267 A LEU 280 A LEU 281 BINDING SITE FOR RESIDUE DTT A 290 A DTT 290 Software 10 BINDING SITE FOR RESIDUE GOL A 291 A GOL 291 Software 5 BINDING SITE FOR RESIDUE GOL A 292 A GOL 292 Software 2 A GLY 8 A GLY 9 10 1_555 A THR 9 A THR 10 10 1_555 A GLN 10 A GLN 11 10 1_555 A ASN 11 A ASN 12 10 1_555 A ASN 89 A ASN 90 10 1_555 A GLY 90 A GLY 91 10 1_555 A VAL 91 A VAL 92 10 1_555 A ARG 92 A ARG 93 10 1_555 A VAL 93 A VAL 94 10 1_555 A SER 225 A SER 226 10 1_555 A ASP 71 A ASP 72 5 1_555 A TRP 72 A TRP 73 5 1_555 A ARG 106 A ARG 107 5 1_555 A PHE 109 A PHE 110 5 1_555 A VAL 110 A VAL 111 5 1_555 A HIS 123 A HIS 124 2 1_555 A ARG 269 A ARG 270 2 1_555 179 P 65 2 2