0.025699 0.000000 0.004159 0.000000 0.022748 0.000000 0.000000 0.000000 0.012631 0.00000 0.00000 0.00000 Stogios, P.J. Wawrzak, Z. Evdokimova, E. Minasov, G. Egorova, O. Di Leo, R. Kudritska, M. Yim, V. Meziane-Cherif, D. Courvalin, P. Savchenko, A. Anderson, W.F. Center for Structural Genomics of Infectious Diseases (CSGID) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 99.19 90.00 38.912 43.960 80.199 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 Cl -1 35.453 CHLORIDE ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C2 H6 O2 62.068 1,2-ETHANEDIOL ETHYLENE GLYCOL 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 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 O4 S -2 96.063 SULFATE ION non-polymer 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 Zn 2 65.409 ZINC ION non-polymer US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 111 5872 5877 10.1073/pnas.1402259111 24711382 Structural basis for the evolution of vancomycin resistance D,D-peptidases. 2014 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 mirrors CCD 2011-07-09 MARMOSAIC 300 mm CCD SI {1,1,1} SINGLE WAVELENGTH M x-ray 1 0.97918 1.0 21-ID-D APS 0.97918 SYNCHROTRON APS BEAMLINE 21-ID-D 29775.939 D,D-dipeptidase/D,D-carboxypeptidase 1 man polymer 65.409 ZINC ION 1 syn non-polymer 35.453 CHLORIDE ION 1 syn non-polymer 96.063 SULFATE ION 1 syn non-polymer 62.068 1,2-ETHANEDIOL 10 syn non-polymer 92.094 GLYCEROL 3 syn non-polymer 18.015 water 187 nat water D,D-peptidase, VanXYG no yes G(MSE)(MSE)KTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNIL(MSE)KRDVANVLQLIFEKISAGNSI VPVSGYRSLEEQTAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGF TQRYARDKEEITGISHEPWHFRYVGYPHSKI(MSE)QENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDK TLIKIPENCVYQISGNNIDGFVVTIWRKTDD GMMKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILMKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQ TAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEIT GISHEPWHFRYVGYPHSKIMQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGN NIDGFVVTIWRKTDD A IDP91774 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 BM4518 sample vanXYG, vanYG2 1351 Enterococcus faecalis 469008 Escherichia coli BL21(DE3) plasmid p15Tv lic 1 2.27 45.91 VAPOR DIFFUSION, SITTING DROP 6.3 0.2 M ammonium sulfate, 0.1 M sodium cacodylate, 30% PEG 8K, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K 298 Center for Structural Genomics of Infectious Diseases CSGID NIAID, National Institute of Allergy and Infectious Diseases repository Initial release Structure summary Structure summary Other Database references Database references 1 0 2012-05-23 1 1 2013-10-02 1 2 2013-10-16 1 3 2014-01-22 1 4 2014-04-23 1 5 2014-05-14 Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg in complex with D-Ala-D-Ala phosphinate analog Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Ala-D-Ala phosphinate analog Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine Crystal structure of vancomycin resistance D,D-dipeptidase/D,D-pentapeptidase VanXYc D59S mutant in complex with D-Alanine-D-Alanine and copper (II) Y RCSB Y RCSB 2012-05-15 REL REL ZN ZINC ION CL CHLORIDE ION SO4 SULFATE ION EDO 1,2-ETHANEDIOL GOL GLYCEROL HOH water ZN 1 2 ZN ZN 301 A CL 2 3 CL CL 302 A SO4 3 4 SO4 SO4 303 A EDO 9 5 EDO EDO 304 A EDO 10 5 EDO EDO 305 A EDO 11 5 EDO EDO 306 A EDO 12 5 EDO EDO 307 A EDO 13 5 EDO EDO 308 A EDO 14 5 EDO EDO 309 A EDO 15 5 EDO EDO 310 A EDO 16 5 EDO EDO 311 A EDO 17 5 EDO EDO 312 A EDO 18 5 EDO EDO 313 A GOL 19 6 GOL GOL 314 A GOL 20 6 GOL GOL 315 A GOL 21 6 GOL GOL 316 A HOH 2 7 HOH HOH 401 A HOH 3 7 HOH HOH 402 A HOH 4 7 HOH HOH 403 A HOH 5 7 HOH HOH 404 A HOH 6 7 HOH HOH 405 A HOH 7 7 HOH HOH 406 A HOH 8 7 HOH HOH 407 A HOH 9 7 HOH HOH 408 A HOH 10 7 HOH HOH 409 A HOH 11 7 HOH HOH 410 A HOH 12 7 HOH HOH 411 A HOH 13 7 HOH HOH 412 A HOH 14 7 HOH HOH 413 A HOH 15 7 HOH HOH 414 A HOH 16 7 HOH HOH 415 A HOH 17 7 HOH HOH 416 A HOH 18 7 HOH HOH 417 A HOH 19 7 HOH HOH 418 A HOH 20 7 HOH HOH 419 A HOH 21 7 HOH HOH 420 A HOH 23 7 HOH HOH 421 A HOH 24 7 HOH HOH 422 A HOH 25 7 HOH HOH 423 A HOH 26 7 HOH HOH 424 A HOH 27 7 HOH HOH 425 A HOH 28 7 HOH HOH 426 A HOH 29 7 HOH HOH 427 A HOH 30 7 HOH HOH 428 A HOH 31 7 HOH HOH 429 A HOH 32 7 HOH HOH 430 A HOH 33 7 HOH HOH 431 A HOH 34 7 HOH HOH 432 A HOH 35 7 HOH HOH 433 A HOH 36 7 HOH HOH 434 A HOH 37 7 HOH HOH 435 A HOH 38 7 HOH HOH 436 A HOH 39 7 HOH HOH 437 A HOH 40 7 HOH HOH 438 A HOH 41 7 HOH HOH 439 A HOH 44 7 HOH HOH 440 A HOH 45 7 HOH HOH 441 A HOH 46 7 HOH HOH 442 A HOH 47 7 HOH HOH 443 A HOH 48 7 HOH HOH 444 A HOH 49 7 HOH HOH 445 A HOH 51 7 HOH HOH 446 A HOH 52 7 HOH HOH 447 A HOH 53 7 HOH HOH 448 A HOH 54 7 HOH HOH 449 A HOH 55 7 HOH HOH 450 A HOH 56 7 HOH HOH 451 A HOH 57 7 HOH HOH 452 A HOH 58 7 HOH HOH 453 A HOH 59 7 HOH HOH 454 A HOH 60 7 HOH HOH 455 A HOH 62 7 HOH HOH 456 A HOH 63 7 HOH HOH 457 A HOH 65 7 HOH HOH 458 A HOH 66 7 HOH HOH 459 A HOH 67 7 HOH HOH 460 A HOH 68 7 HOH HOH 461 A HOH 70 7 HOH HOH 462 A HOH 72 7 HOH HOH 463 A HOH 73 7 HOH HOH 464 A HOH 74 7 HOH HOH 465 A HOH 75 7 HOH HOH 466 A HOH 76 7 HOH HOH 467 A HOH 77 7 HOH HOH 468 A HOH 78 7 HOH HOH 469 A HOH 79 7 HOH HOH 470 A HOH 80 7 HOH HOH 471 A HOH 81 7 HOH HOH 472 A HOH 83 7 HOH HOH 473 A HOH 86 7 HOH HOH 474 A HOH 87 7 HOH HOH 475 A HOH 88 7 HOH HOH 476 A HOH 89 7 HOH HOH 477 A HOH 90 7 HOH HOH 478 A HOH 91 7 HOH HOH 479 A HOH 92 7 HOH HOH 480 A HOH 93 7 HOH HOH 481 A HOH 94 7 HOH HOH 482 A HOH 95 7 HOH HOH 483 A HOH 96 7 HOH HOH 484 A HOH 97 7 HOH HOH 485 A HOH 98 7 HOH HOH 486 A HOH 99 7 HOH HOH 487 A HOH 100 7 HOH HOH 488 A HOH 101 7 HOH HOH 489 A HOH 102 7 HOH HOH 490 A HOH 103 7 HOH HOH 491 A HOH 106 7 HOH HOH 492 A HOH 108 7 HOH HOH 493 A HOH 109 7 HOH HOH 494 A HOH 110 7 HOH HOH 495 A HOH 112 7 HOH HOH 496 A HOH 113 7 HOH HOH 497 A HOH 114 7 HOH HOH 498 A HOH 115 7 HOH HOH 499 A HOH 116 7 HOH HOH 500 A HOH 122 7 HOH HOH 501 A HOH 123 7 HOH HOH 502 A HOH 124 7 HOH HOH 503 A HOH 127 7 HOH HOH 504 A HOH 129 7 HOH HOH 505 A HOH 130 7 HOH HOH 506 A HOH 132 7 HOH HOH 507 A HOH 133 7 HOH HOH 508 A HOH 135 7 HOH HOH 509 A HOH 137 7 HOH HOH 510 A HOH 138 7 HOH HOH 511 A HOH 140 7 HOH HOH 512 A HOH 141 7 HOH HOH 513 A HOH 142 7 HOH HOH 514 A HOH 143 7 HOH HOH 515 A HOH 144 7 HOH HOH 516 A HOH 145 7 HOH HOH 517 A HOH 146 7 HOH HOH 518 A HOH 149 7 HOH HOH 519 A HOH 150 7 HOH HOH 520 A HOH 151 7 HOH HOH 521 A HOH 152 7 HOH HOH 522 A HOH 153 7 HOH HOH 523 A HOH 154 7 HOH HOH 524 A HOH 155 7 HOH HOH 525 A HOH 156 7 HOH HOH 526 A HOH 157 7 HOH HOH 527 A HOH 158 7 HOH HOH 528 A HOH 159 7 HOH HOH 529 A HOH 160 7 HOH HOH 530 A HOH 161 7 HOH HOH 531 A HOH 162 7 HOH HOH 532 A HOH 168 7 HOH HOH 533 A HOH 169 7 HOH HOH 534 A HOH 172 7 HOH HOH 535 A HOH 173 7 HOH HOH 536 A HOH 174 7 HOH HOH 537 A HOH 179 7 HOH HOH 538 A HOH 183 7 HOH HOH 539 A HOH 184 7 HOH HOH 540 A HOH 188 7 HOH HOH 541 A HOH 189 7 HOH HOH 542 A HOH 197 7 HOH HOH 543 A HOH 203 7 HOH HOH 544 A HOH 205 7 HOH HOH 545 A HOH 207 7 HOH HOH 546 A HOH 208 7 HOH HOH 547 A HOH 209 7 HOH HOH 548 A HOH 212 7 HOH HOH 549 A HOH 213 7 HOH HOH 550 A HOH 214 7 HOH HOH 551 A HOH 215 7 HOH HOH 552 A HOH 217 7 HOH HOH 553 A HOH 218 7 HOH HOH 554 A HOH 219 7 HOH HOH 555 A HOH 221 7 HOH HOH 556 A HOH 222 7 HOH HOH 557 A HOH 225 7 HOH HOH 558 A HOH 228 7 HOH HOH 559 A HOH 229 7 HOH HOH 560 A HOH 230 7 HOH HOH 561 A HOH 231 7 HOH HOH 562 A HOH 233 7 HOH HOH 563 A HOH 234 7 HOH HOH 564 A HOH 236 7 HOH HOH 565 A HOH 238 7 HOH HOH 566 A HOH 239 7 HOH HOH 567 A HOH 241 7 HOH HOH 568 A HOH 243 7 HOH HOH 569 A HOH 244 7 HOH HOH 570 A HOH 245 7 HOH HOH 571 A HOH 246 7 HOH HOH 572 A HOH 247 7 HOH HOH 573 A HOH 249 7 HOH HOH 574 A HOH 251 7 HOH HOH 575 A HOH 252 7 HOH HOH 576 A HOH 253 7 HOH HOH 577 A HOH 254 7 HOH HOH 578 A HOH 255 7 HOH HOH 579 A HOH 257 7 HOH HOH 580 A HOH 259 7 HOH HOH 581 A HOH 262 7 HOH HOH 582 A HOH 264 7 HOH HOH 583 A HOH 265 7 HOH HOH 584 A HOH 266 7 HOH HOH 585 A HOH 267 7 HOH HOH 586 A HOH 268 7 HOH HOH 587 A GLY 0 n 1 GLY 0 A MSE 1 n 2 MSE 1 A MSE 2 n 3 MSE 2 A LYS 3 n 4 LYS 3 A THR 4 n 5 THR 4 A ILE 5 n 6 ILE 5 A GLU 6 n 7 GLU 6 A LEU 7 n 8 LEU 7 A GLU 8 n 9 GLU 8 A LYS 9 n 10 LYS 9 A GLU 10 n 11 GLU 10 A GLU 11 n 12 GLU 11 A ILE 12 n 13 ILE 12 A TYR 13 n 14 TYR 13 A CYS 14 n 15 CYS 14 A GLY 15 n 16 GLY 15 A ASN 16 n 17 ASN 16 A LEU 17 n 18 LEU 17 A LEU 18 n 19 LEU 18 A LEU 19 n 20 LEU 19 A VAL 20 n 21 VAL 20 A ASN 21 n 22 ASN 21 A LYS 22 n 23 LYS 22 A ASN 23 n 24 ASN 23 A TYR 24 n 25 TYR 24 A PRO 25 n 26 PRO 25 A LEU 26 n 27 LEU 26 A ARG 27 n 28 ARG 27 A ASP 28 n 29 ASP 28 A ASN 29 n 30 ASN 29 A ASN 30 n 31 ASN 30 A VAL 31 n 32 VAL 31 A LYS 32 n 33 LYS 32 A GLY 33 n 34 GLY 33 A LEU 34 n 35 LEU 34 A VAL 35 n 36 VAL 35 A PRO 36 n 37 PRO 36 A ALA 37 n 38 ALA 37 A ASP 38 n 39 ASP 38 A ILE 39 n 40 ILE 39 A ARG 40 n 41 ARG 40 A PHE 41 n 42 PHE 41 A PRO 42 n 43 PRO 42 A ASN 43 n 44 ASN 43 A ILE 44 n 45 ILE 44 A LEU 45 n 46 LEU 45 A MSE 46 n 47 MSE 46 A LYS 47 n 48 LYS 47 A ARG 48 n 49 ARG 48 A ASP 49 n 50 ASP 49 A VAL 50 n 51 VAL 50 A ALA 51 n 52 ALA 51 A ASN 52 n 53 ASN 52 A VAL 53 n 54 VAL 53 A LEU 54 n 55 LEU 54 A GLN 55 n 56 GLN 55 A LEU 56 n 57 LEU 56 A ILE 57 n 58 ILE 57 A PHE 58 n 59 PHE 58 A GLU 59 n 60 GLU 59 A LYS 60 n 61 LYS 60 A ILE 61 n 62 ILE 61 A SER 62 n 63 SER 62 A ALA 63 n 64 ALA 63 A GLY 64 n 65 GLY 64 A ASN 65 n 66 ASN 65 A SER 66 n 67 SER 66 A ILE 67 n 68 ILE 67 A VAL 68 n 69 VAL 68 A PRO 69 n 70 PRO 69 A VAL 70 n 71 VAL 70 A SER 71 n 72 SER 71 A GLY 72 n 73 GLY 72 A TYR 73 n 74 TYR 73 A ARG 74 n 75 ARG 74 A SER 75 n 76 SER 75 A LEU 76 n 77 LEU 76 A GLU 77 n 78 GLU 77 A GLU 78 n 79 GLU 78 A GLN 79 n 80 GLN 79 A THR 80 n 81 THR 80 A ALA 81 n 82 ALA 81 A ILE 82 n 83 ILE 82 A TYR 83 n 84 TYR 83 A ASP 84 n 85 ASP 84 A GLY 85 n 86 GLY 85 A SER 86 n 87 SER 86 A LEU 87 n 88 LEU 87 A LYS 88 n 89 LYS 88 A ASP 89 n 90 ASP 89 A ASN 90 n 91 ASN 90 A GLY 91 n 92 GLY 91 A GLU 92 n 93 GLU 92 A ASP 93 n 94 ASP 93 A PHE 94 n 95 PHE 94 A THR 95 n 96 THR 95 A ARG 96 n 97 ARG 96 A LYS 97 n 98 LYS 97 A TYR 98 n 99 TYR 98 A VAL 99 n 100 VAL 99 A ALA 100 n 101 ALA 100 A LEU 101 n 102 LEU 101 A PRO 102 n 103 PRO 102 A ASN 103 n 104 ASN 103 A HIS 104 n 105 HIS 104 A SER 105 n 106 SER 105 A GLU 106 n 107 GLU 106 A HIS 107 n 108 HIS 107 A GLN 108 n 109 GLN 108 A THR 109 n 110 THR 109 A GLY 110 n 111 GLY 110 A LEU 111 n 112 LEU 111 A ALA 112 n 113 ALA 112 A ILE 113 n 114 ILE 113 A ASP 114 n 115 ASP 114 A LEU 115 n 116 LEU 115 A GLY 116 n 117 GLY 116 A LEU 117 n 118 LEU 117 A ASN 118 n 119 ASN 118 A LYS 119 n 120 LYS 119 A LYS 120 n 121 LYS 120 A ASP 121 n 122 ASP 121 A ILE 122 n 123 ILE 122 A ASP 123 n 124 ASP 123 A PHE 124 n 125 PHE 124 A ILE 125 n 126 ILE 125 A ARG 126 n 127 ARG 126 A PRO 127 n 128 PRO 127 A ASP 128 n 129 ASP 128 A PHE 129 n 130 PHE 129 A PRO 130 n 131 PRO 130 A TYR 131 n 132 TYR 131 A ASP 132 n 133 ASP 132 A GLY 133 n 134 GLY 133 A ILE 134 n 135 ILE 134 A CYS 135 n 136 CYS 135 A ASP 136 n 137 ASP 136 A GLU 137 n 138 GLU 137 A PHE 138 n 139 PHE 138 A ARG 139 n 140 ARG 139 A ARG 140 n 141 ARG 140 A ALA 141 n 142 ALA 141 A ALA 142 n 143 ALA 142 A PRO 143 n 144 PRO 143 A ASP 144 n 145 ASP 144 A TYR 145 n 146 TYR 145 A GLY 146 n 147 GLY 146 A PHE 147 n 148 PHE 147 A THR 148 n 149 THR 148 A GLN 149 n 150 GLN 149 A ARG 150 n 151 ARG 150 A TYR 151 n 152 TYR 151 A ALA 152 n 153 ALA 152 A ARG 153 n 154 ARG 153 A ASP 154 n 155 ASP 154 A LYS 155 n 156 LYS 155 A GLU 156 n 157 GLU 156 A GLU 157 n 158 GLU 157 A ILE 158 n 159 ILE 158 A THR 159 n 160 THR 159 A GLY 160 n 161 GLY 160 A ILE 161 n 162 ILE 161 A SER 162 n 163 SER 162 A HIS 163 n 164 HIS 163 A GLU 164 n 165 GLU 164 A PRO 165 n 166 PRO 165 A TRP 166 n 167 TRP 166 A HIS 167 n 168 HIS 167 A PHE 168 n 169 PHE 168 A ARG 169 n 170 ARG 169 A TYR 170 n 171 TYR 170 A VAL 171 n 172 VAL 171 A GLY 172 n 173 GLY 172 A TYR 173 n 174 TYR 173 A PRO 174 n 175 PRO 174 A HIS 175 n 176 HIS 175 A SER 176 n 177 SER 176 A LYS 177 n 178 LYS 177 A ILE 178 n 179 ILE 178 A MSE 179 n 180 MSE 179 A GLN 180 n 181 GLN 180 A GLU 181 n 182 GLU 181 A ASN 182 n 183 ASN 182 A GLY 183 n 184 GLY 183 A PHE 184 n 185 PHE 184 A SER 185 n 186 SER 185 A LEU 186 n 187 LEU 186 A GLU 187 n 188 GLU 187 A GLU 188 n 189 GLU 188 A TYR 189 n 190 TYR 189 A THR 190 n 191 THR 190 A GLN 191 n 192 GLN 191 A PHE 192 n 193 PHE 192 A ILE 193 n 194 ILE 193 A LYS 194 n 195 LYS 194 A ALA 195 n 196 ALA 195 A TYR 196 n 197 TYR 196 A LEU 197 n 198 LEU 197 A GLU 198 n 199 GLU 198 A ASP 199 n 200 ASP 199 A ASN 200 n 201 ASN 200 A LYS 201 n 202 LYS 201 A TYR 202 n 203 TYR 202 A LEU 203 n 204 LEU 203 A PHE 204 n 205 PHE 204 A GLU 205 n 206 GLU 205 A GLN 206 n 207 GLN 206 A ALA 207 n 208 ALA 207 A HIS 208 n 209 HIS 208 A ARG 209 n 210 ARG 209 A ALA 210 n 211 ALA 210 A GLU 211 n 212 GLU 211 A ILE 212 n 213 ILE 212 A GLU 213 n 214 GLU 213 A ILE 214 n 215 ILE 214 A TYR 215 n 216 TYR 215 A TYR 216 n 217 TYR 216 A VAL 217 n 218 VAL 217 A PRO 218 n 219 PRO 218 A ALA 219 n 220 ALA 219 A LYS 220 n 221 LYS 220 A ASP 221 n 222 ASP 221 A ASP 222 n 223 ASP 222 A LYS 223 n 224 LYS 223 A THR 224 n 225 THR 224 A LEU 225 n 226 LEU 225 A ILE 226 n 227 ILE 226 A LYS 227 n 228 LYS 227 A ILE 228 n 229 ILE 228 A PRO 229 n 230 PRO 229 A GLU 230 n 231 GLU 230 A ASN 231 n 232 ASN 231 A CYS 232 n 233 CYS 232 A VAL 233 n 234 VAL 233 A TYR 234 n 235 TYR 234 A GLN 235 n 236 GLN 235 A ILE 236 n 237 ILE 236 A SER 237 n 238 SER 237 A GLY 238 n 239 GLY 238 A ASN 239 n 240 ASN 239 A ASN 240 n 241 ASN 240 A ILE 241 n 242 ILE 241 A ASP 242 n 243 ASP 242 A GLY 243 n 244 GLY 243 A PHE 244 n 245 PHE 244 A VAL 245 n 246 VAL 245 A VAL 246 n 247 VAL 246 A THR 247 n 248 THR 247 A ILE 248 n 249 ILE 248 A TRP 249 n 250 TRP 249 A ARG 250 n 251 ARG 250 A n 252 251 A n 253 252 A n 254 253 A n 255 254 A 0.3823 0.0117 0.5165 0.7702 -0.0827 1.4629 -0.0166 -0.3294 -0.2666 0.1715 0.0401 0.1086 0.1831 -0.0589 -0.0657 0.1352 -0.0144 0.0118 0.1233 0.0325 0.1346 refined -13.4764 -13.8820 -18.1936 X-RAY DIFFRACTION 1.0575 -0.4240 -0.5374 1.6291 0.7564 3.0137 0.0413 -0.0201 0.0131 -0.0517 -0.0586 0.0985 0.0093 -0.1347 0.0057 0.0502 -0.0142 -0.0138 0.0542 0.0050 0.1032 refined -17.2558 -5.3482 -31.1827 X-RAY DIFFRACTION 2.6162 -0.6600 -0.0608 2.2842 -0.2919 2.1523 0.0153 -0.0502 0.1704 -0.0675 0.0561 0.0946 -0.2049 -0.1041 -0.0282 0.0715 -0.0035 0.0197 0.0411 -0.0185 0.0841 refined -11.8754 3.1163 -23.7725 X-RAY DIFFRACTION 2.7849 0.4257 0.4265 3.8666 -0.5094 3.0980 -0.0539 -0.6402 -0.0715 0.7326 -0.0311 0.0969 0.2433 -0.0655 0.0156 0.1725 0.0405 -0.0385 0.2656 0.0223 0.0305 refined -3.1852 -8.8349 -5.4101 X-RAY DIFFRACTION X-RAY DIFFRACTION 1 chain A and resi 0:50 X-RAY DIFFRACTION 2 chain A and resi 51:116 X-RAY DIFFRACTION 3 chain A and resi 117:194 X-RAY DIFFRACTION 4 chain A and resi 195:250 author_and_software_defined_assembly PISA 1 monomeric A ASP 114 A OD1 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 A HIS 167 A ND1 HIS 168 1_555 91.9 A ASP 114 A OD1 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 A HOH 418 R O HOH 1_555 99.2 A HIS 167 A ND1 HIS 168 1_555 A ZN 301 B ZN ZN 1_555 A HOH 418 R O HOH 1_555 94.0 A ASP 114 A OD1 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 A HIS 107 A NE2 HIS 108 1_555 95.7 A HIS 167 A ND1 HIS 168 1_555 A ZN 301 B ZN ZN 1_555 A HIS 107 A NE2 HIS 108 1_555 101.5 A HOH 418 R O HOH 1_555 A ZN 301 B ZN ZN 1_555 A HIS 107 A NE2 HIS 108 1_555 158.1 A ASP 114 A OD1 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 A ASP 114 A OD2 ASP 115 1_555 55.2 A HIS 167 A ND1 HIS 168 1_555 A ZN 301 B ZN ZN 1_555 A ASP 114 A OD2 ASP 115 1_555 147.1 A HOH 418 R O HOH 1_555 A ZN 301 B ZN ZN 1_555 A ASP 114 A OD2 ASP 115 1_555 92.2 A HIS 107 A NE2 HIS 108 1_555 A ZN 301 B ZN ZN 1_555 A ASP 114 A OD2 ASP 115 1_555 83.3 A ASP 114 A OD1 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 A SO4 303 D O2 SO4 1_555 151.7 A HIS 167 A ND1 HIS 168 1_555 A ZN 301 B ZN ZN 1_555 A SO4 303 D O2 SO4 1_555 116.4 A HOH 418 R O HOH 1_555 A ZN 301 B ZN ZN 1_555 A SO4 303 D O2 SO4 1_555 79.0 A HIS 107 A NE2 HIS 108 1_555 A ZN 301 B ZN ZN 1_555 A SO4 303 D O2 SO4 1_555 80.2 A ASP 114 A OD2 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 A SO4 303 D O2 SO4 1_555 96.5 A MSE 1 SELENOMETHIONINE A MSE 2 MET A MSE 2 SELENOMETHIONINE A MSE 3 MET A MSE 46 SELENOMETHIONINE A MSE 47 MET A MSE 179 SELENOMETHIONINE A MSE 180 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 3 A N LYS 4 A O ILE 228 A O ILE 229 A N VAL 35 A N VAL 36 A O MSE 46 A O MSE 47 A N VAL 70 A N VAL 71 A O ASP 114 A O ASP 115 A N ILE 113 A N ILE 114 A O PHE 168 A O PHE 169 A O ARG 169 A O ARG 170 A N THR 148 A N THR 149 A N PHE 204 A N PHE 205 A O ILE 212 A O ILE 213 A N GLU 213 A N GLU 214 A O ILE 248 A O ILE 249 A O TRP 249 A O TRP 250 A N VAL 233 A N VAL 234 1 A LYS 251 A LYS 252 1 Y 1 A THR 252 A THR 253 1 Y 1 A ASP 253 A ASP 254 1 Y 1 A ASP 254 A ASP 255 1 Y 1 A A O4 O SO4 HOH 303 483 2.17 1 A ASP 121 -93.20 51.54 1 A TYR 131 -96.39 39.91 1 A HIS 163 -37.40 122.11 1 A ASN 200 -155.63 67.33 1 A ASN 200 -151.60 59.19 1 A GLN 206 -103.08 -79.85 1 A ALA 207 -177.20 105.97 1 A HIS 208 -26.39 117.57 1 A ARG 209 56.21 -140.97 1 A ASP 222 -116.75 -96.12 1 A ASN 231 -78.69 39.66 1 A ILE 241 -127.26 -58.31 1 A ASP 242 -155.66 -0.20 -1.7143 0.0000 -4.2779 1.3494 -0.0000 0.3648 0.1864 0.1536 0.1554 1.950 39.584 949 19734 4.99 98.35 0.19 random 1 THROUGHOUT 1.35 SAD 18.50 0.73 1.00 ML FLAT BULK SOLVENT MODEL 48.654 0.399 1.950 39.584 187 2306 65 0 2054 0.016 2201 1.494 2966 14.268 840 0.116 310 0.007 386 0.2775 0.2171 2.0027 123 2747 98.00 0.2068 0.1947 2.0617 146 2708 98.00 0.2173 0.1755 2.1282 144 2768 98.00 0.2052 0.1596 2.2043 137 2715 98.00 0.2152 0.1600 2.2925 146 2811 98.00 0.1972 0.1557 2.3968 151 2673 98.00 0.2262 0.1580 2.5232 151 2766 98.00 0.1956 0.1529 2.6812 136 2757 99.00 0.1882 0.1515 2.8882 152 2757 99.00 0.1934 0.1497 3.1787 153 2758 99.00 0.1718 0.1439 3.6384 145 2772 99.00 0.1564 0.1227 4.5829 147 2756 99.00 0.1556 0.1596 39.5926 144 2738 98.00 1.95 79.17 4F78 19747 0 -3 0.078 1 10.6 3.3 100.0 0.329 1.95 2.06 3.6 2850 1 3.3 100.0 data collection HKL-3000 model building PHENIX (phenix.autosol) refinement PHENIX (phenix.refine: 1.7.3_928) data reduction XDS data scaling SCALA phasing PHENIX Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg Crystal Structure of Vancomycin Resistance D,D-dipeptidase VanXYg 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N 6 N N 6 N N 6 N N 7 N N A GLU 10 A GLU 11 HELX_P A CYS 14 A CYS 15 5 1 5 A ARG 48 A ARG 49 HELX_P A ILE 61 A ILE 62 1 2 14 A SER 75 A SER 76 HELX_P A GLY 91 A GLY 92 1 3 17 A GLY 91 A GLY 92 HELX_P A VAL 99 A VAL 100 1 4 9 A SER 105 A SER 106 HELX_P A GLY 110 A GLY 111 5 5 6 A ASP 132 A ASP 133 HELX_P A ALA 142 A ALA 143 1 6 11 A PRO 143 A PRO 144 HELX_P A TYR 145 A TYR 146 5 7 3 A ALA 152 A ALA 153 HELX_P A ASP 154 A ASP 155 5 8 3 A LYS 155 A LYS 156 HELX_P A GLY 160 A GLY 161 1 9 6 A PRO 174 A PRO 175 HELX_P A GLY 183 A GLY 184 1 10 10 A SER 185 A SER 186 HELX_P A LYS 194 A LYS 195 1 11 10 covale 1.335 A GLY 0 A C GLY 1 1_555 A MSE 1 A N MSE 2 1_555 covale 1.331 A MSE 1 A C MSE 2 1_555 A MSE 2 A N MSE 3 1_555 covale 1.328 A MSE 2 A C MSE 3 1_555 A LYS 3 A N LYS 4 1_555 covale 1.328 A A LEU 45 A C LEU 46 1_555 A MSE 46 A N MSE 47 1_555 covale 1.336 B A LEU 45 A C LEU 46 1_555 A MSE 46 A N MSE 47 1_555 covale 1.326 A A MSE 46 A C MSE 47 1_555 A LYS 47 A N LYS 48 1_555 covale 1.333 B A MSE 46 A C MSE 47 1_555 A LYS 47 A N LYS 48 1_555 covale 1.329 A ILE 178 A C ILE 179 1_555 A MSE 179 A N MSE 180 1_555 covale 1.327 A MSE 179 A C MSE 180 1_555 A GLN 180 A N GLN 181 1_555 metalc 2.180 A ASP 114 A OD1 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.192 A HIS 167 A ND1 HIS 168 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.205 A ZN 301 B ZN ZN 1_555 A HOH 418 R O HOH 1_555 metalc 2.228 A HIS 107 A NE2 HIS 108 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.558 A ASP 114 A OD2 ASP 115 1_555 A ZN 301 B ZN ZN 1_555 metalc 2.700 A ZN 301 B ZN ZN 1_555 A SO4 303 D O2 SO4 1_555 HYDROLASE CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, CSGID, NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES, NIAID, ALPHA+BETA PROTEIN, METALLOPEPTIDASE, HEDGEHOG/DD-PEPTIDASE FOLD, MEROPS M15B SUBFAMILY, ZN2+-DEPENDENT D, D-DIPEPTIDASE, VANCOMYCIN RESISTANCE, D-ALANINE-D-ALANINE, HYDROLASE A TYR 173 A TYR 174 1 A PRO 174 A PRO 175 4.71 A HIS 208 A HIS 209 1 A ARG 209 A ARG 210 -10.50 Q9KHL8_ENTFL UNP 1 1 Q9KHL8 MMKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILMKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQT AIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEITG ISHEPWHFRYVGYPHSKIMQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGNN IDGFVVTIWRKTDD 1 254 4F78 1 254 Q9KHL8 A 1 2 255 1 EXPRESSION TAG GLY 0 4F78 A Q9KHL8 UNP 1 2 2 4 4 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A MSE 2 A MSE 3 A GLU 8 A GLU 9 A LYS 223 A LYS 224 A PRO 229 A PRO 230 A LEU 34 A LEU 35 A PRO 36 A PRO 37 A LEU 45 A LEU 46 A LYS 47 A LYS 48 A ILE 67 A ILE 68 A SER 71 A SER 72 A ALA 112 A ALA 113 A LEU 117 A LEU 118 A HIS 167 A HIS 168 A TYR 170 A TYR 171 A PHE 147 A PHE 148 A GLN 149 A GLN 150 A TYR 202 A TYR 203 A GLU 205 A GLU 206 A GLU 211 A GLU 212 A PRO 218 A PRO 219 A GLY 243 A GLY 244 A TRP 249 A TRP 250 A VAL 233 A VAL 234 A GLY 238 A GLY 239 BINDING SITE FOR RESIDUE ZN A 301 Software 5 BINDING SITE FOR RESIDUE CL A 302 Software 4 BINDING SITE FOR RESIDUE SO4 A 303 Software 11 BINDING SITE FOR RESIDUE EDO A 304 Software 3 BINDING SITE FOR RESIDUE EDO A 305 Software 7 BINDING SITE FOR RESIDUE EDO A 306 Software 3 BINDING SITE FOR RESIDUE EDO A 307 Software 5 BINDING SITE FOR RESIDUE EDO A 308 Software 2 BINDING SITE FOR RESIDUE EDO A 309 Software 4 BINDING SITE FOR RESIDUE EDO A 310 Software 5 BINDING SITE FOR RESIDUE EDO A 311 Software 4 BINDING SITE FOR RESIDUE EDO A 312 Software 4 BINDING SITE FOR RESIDUE EDO A 313 Software 3 BINDING SITE FOR RESIDUE GOL A 314 Software 3 BINDING SITE FOR RESIDUE GOL A 315 Software 3 BINDING SITE FOR RESIDUE GOL A 316 Software 7 A HIS 107 A HIS 108 5 1_555 A ASP 114 A ASP 115 5 1_555 A HIS 167 A HIS 168 5 1_555 A SO4 303 D SO4 5 1_555 A HOH 418 R HOH 5 1_555 A MSE 2 A MSE 3 4 1_555 A LYS 3 A LYS 4 4 1_555 A THR 4 A THR 5 4 1_555 A LYS 227 A LYS 228 4 1_555 A ARG 74 A ARG 75 11 1_555 A GLN 79 A GLN 80 11 1_555 A VAL 99 A VAL 100 11 1_555 A ALA 100 A ALA 101 11 1_555 A SER 105 A SER 106 11 1_555 A HIS 107 A HIS 108 11 1_555 A HIS 167 A HIS 168 11 1_555 A ZN 301 B ZN 11 1_555 A HOH 424 R HOH 11 1_555 A HOH 460 R HOH 11 1_555 A HOH 483 R HOH 11 1_555 A LYS 120 A LYS 121 3 1_655 A GLU 157 A GLU 158 3 1_555 A EDO 310 K EDO 3 1_555 A PRO 36 A PRO 37 7 1_555 A ALA 37 A ALA 38 7 1_555 A ASN 52 A ASN 53 7 1_555 A GLN 191 A GLN 192 7 1_455 A HOH 442 R HOH 7 1_455 A HOH 512 R HOH 7 1_455 A HOH 516 R HOH 7 1_555 A GLU 188 A GLU 189 3 1_555 A PHE 192 A PHE 193 3 1_555 A HOH 470 R HOH 3 1_655 A PRO 218 A PRO 219 5 1_555 A EDO 308 I EDO 5 1_555 A HOH 431 R HOH 5 1_555 A HOH 491 R HOH 5 1_555 A HOH 524 R HOH 5 1_555 A ASP 199 A ASP 200 2 1_555 A EDO 307 H EDO 2 1_555 A ASN 21 A ASN 22 4 1_555 A LYS 22 A LYS 23 4 1_555 A ILE 158 A ILE 159 4 1_555 A THR 159 A THR 160 4 1_555 A LYS 97 A LYS 98 5 1_555 A GLY 160 A GLY 161 5 1_555 A ILE 161 A ILE 162 5 1_555 A SER 162 A SER 163 5 1_555 A EDO 304 E EDO 5 1_555 A GLY 91 A GLY 92 4 1_555 A GLU 92 A GLU 93 4 1_555 A ASP 93 A ASP 94 4 1_555 A HOH 420 R HOH 4 1_555 A GLU 181 A GLU 182 4 1_555 A PHE 204 A PHE 205 4 1_555 A GLU 205 A GLU 206 4 1_555 A HOH 584 R HOH 4 1_555 A ASP 144 A ASP 145 3 1_555 A ARG 209 A ARG 210 3 1_555 A HOH 531 R HOH 3 1_555 A ALA 152 A ALA 153 3 1_555 A ARG 153 A ARG 154 3 1_555 A ASP 154 A ASP 155 3 1_555 A ASN 65 A ASN 66 3 1_555 A SER 66 A SER 67 3 1_555 A LYS 155 A LYS 156 3 1_455 A CYS 14 A CYS 15 7 1_555 A GLY 15 A GLY 16 7 1_555 A LEU 18 A LEU 19 7 1_555 A VAL 31 A VAL 32 7 1_555 A THR 109 A THR 110 7 1_555 A HOH 578 R HOH 7 1_555 A HOH 585 R HOH 7 1_555 4 P 1 21 1