0.008080 0.000000 0.000000 0.000000 0.008080 0.000000 0.000000 0.000000 0.020973 0.00000 0.00000 0.00000 Miller, D.J. Jerga, A. Rock, C.O. White, S.W. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 123.760 123.760 47.680 C10 H15 N5 O10 P2 427.201 n ADENOSINE-5'-DIPHOSPHATE non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking 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 Mg 2 24.305 MAGNESIUM ION non-polymer C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Structure STRUE6 2005 0969-2126 16 1036 1046 10.1016/j.str.2008.03.019 18611377 Analysis of the Staphylococcus aureus DgkB Structure Reveals a Common Catalytic Mechanism for the Soluble Diacylglycerol Kinases. 2008 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 170 1 mirrors CCD 2007-03-14 MARMOSAIC 300 mm CCD Si-220 SINGLE WAVELENGTH M x-ray 1 1.0 1.0 22-ID APS 1.0 SYNCHROTRON APS BEAMLINE 22-ID 37899.238 Diacylglycerol Kinase DgkB 2.7.1.107 1 man polymer 24.305 MAGNESIUM ION 1 syn non-polymer 427.201 ADENOSINE-5'-DIPHOSPHATE 1 syn non-polymer 18.015 water 152 nat water no yes (MSE)GSSHHHHHHHSSGLVPRGSH(MSE)(MSE)RKRARIIYNPTSGKEQFKRELPDALIKLEKAGYETSAYATEKIGD ATLEAERA(MSE)HENYDVLIAAGGDGTLNEVVNGIAEKPNRPKLGVIP(MSE)GTVNDFGRALHIPNDI(MSE)GALDV IIEGHSTKVDIGK(MSE)NNRYFINLAAGGQLTQVSYETPSKLKSIVGPFAYYIKGFE(MSE)LPQ(MSE)KAVDLRIEY DGNVFQGEALLFFLGLTNS(MSE)AGFEKLVPDAKLDDGYFTLIIVEKSNLAELGHI(MSE)TLASRGEHTKHPKVIYEK AKAINISSFTDLQLNVDGEYGGKLPANFLNLERHIDVFAPNDIVNEELINNDHVDDNLIEE MGSSHHHHHHHSSGLVPRGSHMMRKRARIIYNPTSGKEQFKRELPDALIKLEKAGYETSAYATEKIGDATLEAERAMHEN YDVLIAAGGDGTLNEVVNGIAEKPNRPKLGVIPMGTVNDFGRALHIPNDIMGALDVIIEGHSTKVDIGKMNNRYFINLAA GGQLTQVSYETPSKLKSIVGPFAYYIKGFEMLPQMKAVDLRIEYDGNVFQGEALLFFLGLTNSMAGFEKLVPDAKLDDGY FTLIIVEKSNLAELGHIMTLASRGEHTKHPKVIYEKAKAINISSFTDLQLNVDGEYGGKLPANFLNLERHIDVFAPNDIV NEELINNDHVDDNLIEE 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 n n n n n n n n n n n n n n n n n n n n n n n 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 SAR1989 Staphylococcus aureus Escherichia coli methionine auxotroph B834 Plasmid pAJ015 1 2.41 48.93 VAPOR DIFFUSION 8.5 drop: 0.1 M Tris pH 8.5, 9% PEG2K MME; well: 0.1 M Tris pH 8.5, 18% PEG2K MME, VAPOR DIFFUSION, temperature 277K 277 repository Initial release Advisory Refinement description Version format compliance 1 0 2008-06-17 1 1 2011-07-13 'Apo form' RCSB Y RCSB 2007-08-07 REL REL MG MAGNESIUM ION ADP ADENOSINE-5'-DIPHOSPHATE HOH water MG 501 2 MG MG 501 A ADP 500 3 ADP ADP 500 A WAT 1 4 HOH HOH 502 A WAT 2 4 HOH HOH 503 A WAT 3 4 HOH HOH 504 A WAT 4 4 HOH HOH 505 A WAT 5 4 HOH HOH 506 A WAT 6 4 HOH HOH 507 A WAT 7 4 HOH HOH 508 A WAT 8 4 HOH HOH 509 A WAT 9 4 HOH HOH 510 A WAT 10 4 HOH HOH 511 A WAT 11 4 HOH HOH 512 A WAT 12 4 HOH HOH 513 A WAT 13 4 HOH HOH 514 A WAT 14 4 HOH HOH 515 A WAT 15 4 HOH HOH 516 A WAT 16 4 HOH HOH 517 A WAT 17 4 HOH HOH 518 A WAT 18 4 HOH HOH 519 A WAT 19 4 HOH HOH 520 A WAT 20 4 HOH HOH 521 A WAT 21 4 HOH HOH 522 A WAT 22 4 HOH HOH 523 A WAT 23 4 HOH HOH 524 A WAT 24 4 HOH HOH 525 A WAT 25 4 HOH HOH 526 A WAT 26 4 HOH HOH 527 A WAT 27 4 HOH HOH 528 A WAT 28 4 HOH HOH 529 A WAT 29 4 HOH HOH 530 A WAT 30 4 HOH HOH 531 A WAT 31 4 HOH HOH 532 A WAT 32 4 HOH HOH 533 A WAT 33 4 HOH HOH 534 A WAT 34 4 HOH HOH 535 A WAT 35 4 HOH HOH 536 A WAT 36 4 HOH HOH 537 A WAT 37 4 HOH HOH 538 A WAT 38 4 HOH HOH 539 A WAT 39 4 HOH HOH 540 A WAT 40 4 HOH HOH 541 A WAT 41 4 HOH HOH 542 A WAT 42 4 HOH HOH 543 A WAT 43 4 HOH HOH 544 A WAT 44 4 HOH HOH 545 A WAT 45 4 HOH HOH 546 A WAT 46 4 HOH HOH 547 A WAT 47 4 HOH HOH 548 A WAT 48 4 HOH HOH 549 A WAT 49 4 HOH HOH 550 A WAT 50 4 HOH HOH 551 A WAT 51 4 HOH HOH 552 A WAT 52 4 HOH HOH 553 A WAT 53 4 HOH HOH 554 A WAT 54 4 HOH HOH 555 A WAT 55 4 HOH HOH 556 A WAT 56 4 HOH HOH 557 A WAT 57 4 HOH HOH 558 A WAT 58 4 HOH HOH 559 A WAT 59 4 HOH HOH 560 A WAT 60 4 HOH HOH 561 A WAT 61 4 HOH HOH 562 A WAT 62 4 HOH HOH 563 A WAT 63 4 HOH HOH 564 A WAT 64 4 HOH HOH 565 A WAT 65 4 HOH HOH 566 A WAT 66 4 HOH HOH 567 A WAT 67 4 HOH HOH 568 A WAT 68 4 HOH HOH 569 A WAT 69 4 HOH HOH 570 A WAT 70 4 HOH HOH 571 A WAT 71 4 HOH HOH 572 A WAT 72 4 HOH HOH 573 A WAT 73 4 HOH HOH 574 A WAT 74 4 HOH HOH 575 A WAT 75 4 HOH HOH 576 A WAT 76 4 HOH HOH 577 A WAT 77 4 HOH HOH 578 A WAT 78 4 HOH HOH 579 A WAT 79 4 HOH HOH 580 A WAT 80 4 HOH HOH 581 A WAT 81 4 HOH HOH 582 A WAT 82 4 HOH HOH 583 A WAT 83 4 HOH HOH 584 A WAT 84 4 HOH HOH 585 A WAT 85 4 HOH HOH 586 A WAT 86 4 HOH HOH 587 A WAT 87 4 HOH HOH 588 A WAT 88 4 HOH HOH 589 A WAT 89 4 HOH HOH 590 A WAT 90 4 HOH HOH 591 A WAT 91 4 HOH HOH 592 A WAT 92 4 HOH HOH 593 A WAT 93 4 HOH HOH 594 A WAT 94 4 HOH HOH 595 A WAT 95 4 HOH HOH 596 A WAT 96 4 HOH HOH 597 A WAT 97 4 HOH HOH 598 A WAT 98 4 HOH HOH 599 A WAT 99 4 HOH HOH 600 A WAT 100 4 HOH HOH 601 A WAT 101 4 HOH HOH 602 A WAT 102 4 HOH HOH 603 A WAT 103 4 HOH HOH 604 A WAT 104 4 HOH HOH 605 A WAT 105 4 HOH HOH 606 A WAT 106 4 HOH HOH 607 A WAT 107 4 HOH HOH 608 A WAT 108 4 HOH HOH 609 A WAT 109 4 HOH HOH 610 A WAT 110 4 HOH HOH 611 A WAT 111 4 HOH HOH 612 A WAT 112 4 HOH HOH 613 A WAT 113 4 HOH HOH 614 A WAT 114 4 HOH HOH 615 A WAT 115 4 HOH HOH 616 A WAT 116 4 HOH HOH 617 A WAT 117 4 HOH HOH 618 A WAT 118 4 HOH HOH 619 A WAT 119 4 HOH HOH 620 A WAT 120 4 HOH HOH 621 A WAT 121 4 HOH HOH 622 A WAT 122 4 HOH HOH 623 A WAT 123 4 HOH HOH 624 A WAT 124 4 HOH HOH 625 A WAT 125 4 HOH HOH 626 A WAT 126 4 HOH HOH 627 A WAT 127 4 HOH HOH 628 A WAT 128 4 HOH HOH 629 A WAT 129 4 HOH HOH 630 A WAT 130 4 HOH HOH 631 A WAT 131 4 HOH HOH 632 A WAT 132 4 HOH HOH 633 A WAT 133 4 HOH HOH 634 A WAT 134 4 HOH HOH 635 A WAT 135 4 HOH HOH 636 A WAT 136 4 HOH HOH 637 A WAT 137 4 HOH HOH 638 A WAT 138 4 HOH HOH 639 A WAT 139 4 HOH HOH 640 A WAT 140 4 HOH HOH 641 A WAT 141 4 HOH HOH 642 A WAT 142 4 HOH HOH 643 A WAT 143 4 HOH HOH 644 A WAT 144 4 HOH HOH 645 A WAT 145 4 HOH HOH 646 A WAT 146 4 HOH HOH 647 A WAT 147 4 HOH HOH 648 A WAT 148 4 HOH HOH 649 A WAT 149 4 HOH HOH 650 A WAT 150 4 HOH HOH 651 A WAT 151 4 HOH HOH 652 A WAT 152 4 HOH HOH 653 A n 1 -21 A n 2 -20 A n 3 -19 A n 4 -18 A n 5 -17 A n 6 -16 A n 7 -15 A n 8 -14 A n 9 -13 A n 10 -12 A n 11 -11 A n 12 -10 A n 13 -9 A n 14 -8 A n 15 -7 A n 16 -6 A n 17 -5 A n 18 -4 A GLY -3 n 19 GLY -3 A ALA -2 n 20 SER -2 A ALA -1 n 21 HIS -1 A ALA 0 n 22 MSE 0 A MSE 1 n 23 MSE 1 A ARG 2 n 24 ARG 2 A LYS 3 n 25 LYS 3 A ARG 4 n 26 ARG 4 A ALA 5 n 27 ALA 5 A ARG 6 n 28 ARG 6 A ILE 7 n 29 ILE 7 A ILE 8 n 30 ILE 8 A TYR 9 n 31 TYR 9 A ASN 10 n 32 ASN 10 A PRO 11 n 33 PRO 11 A THR 12 n 34 THR 12 A SER 13 n 35 SER 13 A GLY 14 n 36 GLY 14 A LYS 15 n 37 LYS 15 A GLU 16 n 38 GLU 16 A GLN 17 n 39 GLN 17 A PHE 18 n 40 PHE 18 A LYS 19 n 41 LYS 19 A ARG 20 n 42 ARG 20 A GLU 21 n 43 GLU 21 A LEU 22 n 44 LEU 22 A PRO 23 n 45 PRO 23 A ASP 24 n 46 ASP 24 A ALA 25 n 47 ALA 25 A LEU 26 n 48 LEU 26 A ILE 27 n 49 ILE 27 A LYS 28 n 50 LYS 28 A LEU 29 n 51 LEU 29 A GLU 30 n 52 GLU 30 A LYS 31 n 53 LYS 31 A ALA 32 n 54 ALA 32 A GLY 33 n 55 GLY 33 A TYR 34 n 56 TYR 34 A GLU 35 n 57 GLU 35 A THR 36 n 58 THR 36 A SER 37 n 59 SER 37 A ALA 38 n 60 ALA 38 A TYR 39 n 61 TYR 39 A ALA 40 n 62 ALA 40 A THR 41 n 63 THR 41 A GLU 42 n 64 GLU 42 A LYS 43 n 65 LYS 43 A ILE 44 n 66 ILE 44 A GLY 45 n 67 GLY 45 A ASP 46 n 68 ASP 46 A ALA 47 n 69 ALA 47 A THR 48 n 70 THR 48 A LEU 49 n 71 LEU 49 A GLU 50 n 72 GLU 50 A ALA 51 n 73 ALA 51 A GLU 52 n 74 GLU 52 A ARG 53 n 75 ARG 53 A ALA 54 n 76 ALA 54 A MSE 55 n 77 MSE 55 A HIS 56 n 78 HIS 56 A GLU 57 n 79 GLU 57 A ASN 58 n 80 ASN 58 A TYR 59 n 81 TYR 59 A ASP 60 n 82 ASP 60 A VAL 61 n 83 VAL 61 A LEU 62 n 84 LEU 62 A ILE 63 n 85 ILE 63 A ALA 64 n 86 ALA 64 A ALA 65 n 87 ALA 65 A GLY 66 n 88 GLY 66 A GLY 67 n 89 GLY 67 A ASP 68 n 90 ASP 68 A GLY 69 n 91 GLY 69 A THR 70 n 92 THR 70 A LEU 71 n 93 LEU 71 A ASN 72 n 94 ASN 72 A GLU 73 n 95 GLU 73 A VAL 74 n 96 VAL 74 A VAL 75 n 97 VAL 75 A ASN 76 n 98 ASN 76 A GLY 77 n 99 GLY 77 A ILE 78 n 100 ILE 78 A ALA 79 n 101 ALA 79 A GLU 80 n 102 GLU 80 A LYS 81 n 103 LYS 81 A PRO 82 n 104 PRO 82 A ASN 83 n 105 ASN 83 A ARG 84 n 106 ARG 84 A PRO 85 n 107 PRO 85 A LYS 86 n 108 LYS 86 A LEU 87 n 109 LEU 87 A GLY 88 n 110 GLY 88 A VAL 89 n 111 VAL 89 A ILE 90 n 112 ILE 90 A PRO 91 n 113 PRO 91 A MSE 92 n 114 MSE 92 A GLY 93 n 115 GLY 93 A THR 94 n 116 THR 94 A VAL 95 n 117 VAL 95 A ASN 96 n 118 ASN 96 A ASP 97 n 119 ASP 97 A PHE 98 n 120 PHE 98 A GLY 99 n 121 GLY 99 A ARG 100 n 122 ARG 100 A ALA 101 n 123 ALA 101 A LEU 102 n 124 LEU 102 A HIS 103 n 125 HIS 103 A ILE 104 n 126 ILE 104 A PRO 105 n 127 PRO 105 A ASN 106 n 128 ASN 106 A ASP 107 n 129 ASP 107 A ILE 108 n 130 ILE 108 A MSE 109 n 131 MSE 109 A GLY 110 n 132 GLY 110 A ALA 111 n 133 ALA 111 A LEU 112 n 134 LEU 112 A ASP 113 n 135 ASP 113 A VAL 114 n 136 VAL 114 A ILE 115 n 137 ILE 115 A ILE 116 n 138 ILE 116 A GLU 117 n 139 GLU 117 A GLY 118 n 140 GLY 118 A HIS 119 n 141 HIS 119 A SER 120 n 142 SER 120 A THR 121 n 143 THR 121 A LYS 122 n 144 LYS 122 A VAL 123 n 145 VAL 123 A ASP 124 n 146 ASP 124 A ILE 125 n 147 ILE 125 A GLY 126 n 148 GLY 126 A LYS 127 n 149 LYS 127 A MSE 128 n 150 MSE 128 A ASN 129 n 151 ASN 129 A ASN 130 n 152 ASN 130 A ARG 131 n 153 ARG 131 A TYR 132 n 154 TYR 132 A PHE 133 n 155 PHE 133 A ILE 134 n 156 ILE 134 A ASN 135 n 157 ASN 135 A LEU 136 n 158 LEU 136 A ALA 137 n 159 ALA 137 A ALA 138 n 160 ALA 138 A GLY 139 n 161 GLY 139 A GLY 140 n 162 GLY 140 A GLN 141 n 163 GLN 141 A LEU 142 n 164 LEU 142 A THR 143 n 165 THR 143 A ALA 144 n 166 GLN 144 A n 167 145 A n 168 146 A n 169 147 A n 170 148 A n 171 149 A n 172 150 A n 173 151 A n 174 152 A n 175 153 A n 176 154 A n 177 155 A n 178 156 A n 179 157 A GLY 158 n 180 GLY 158 A PRO 159 n 181 PRO 159 A PHE 160 n 182 PHE 160 A ALA 161 n 183 ALA 161 A ALA 162 n 184 TYR 162 A TYR 163 n 185 TYR 163 A ILE 164 n 186 ILE 164 A ALA 165 n 187 LYS 165 A GLY 166 n 188 GLY 166 A PHE 167 n 189 PHE 167 A GLU 168 n 190 GLU 168 A MSE 169 n 191 MSE 169 A LEU 170 n 192 LEU 170 A PRO 171 n 193 PRO 171 A GLN 172 n 194 GLN 172 A MSE 173 n 195 MSE 173 A LYS 174 n 196 LYS 174 A ALA 175 n 197 ALA 175 A VAL 176 n 198 VAL 176 A ASP 177 n 199 ASP 177 A LEU 178 n 200 LEU 178 A ARG 179 n 201 ARG 179 A ILE 180 n 202 ILE 180 A GLU 181 n 203 GLU 181 A TYR 182 n 204 TYR 182 A ASP 183 n 205 ASP 183 A GLY 184 n 206 GLY 184 A ASN 185 n 207 ASN 185 A VAL 186 n 208 VAL 186 A PHE 187 n 209 PHE 187 A GLN 188 n 210 GLN 188 A GLY 189 n 211 GLY 189 A GLU 190 n 212 GLU 190 A ALA 191 n 213 ALA 191 A LEU 192 n 214 LEU 192 A LEU 193 n 215 LEU 193 A PHE 194 n 216 PHE 194 A PHE 195 n 217 PHE 195 A LEU 196 n 218 LEU 196 A GLY 197 n 219 GLY 197 A LEU 198 n 220 LEU 198 A THR 199 n 221 THR 199 A ASN 200 n 222 ASN 200 A SER 201 n 223 SER 201 A MSE 202 n 224 MSE 202 A ALA 203 n 225 ALA 203 A GLY 204 n 226 GLY 204 A PHE 205 n 227 PHE 205 A GLU 206 n 228 GLU 206 A LYS 207 n 229 LYS 207 A LEU 208 n 230 LEU 208 A VAL 209 n 231 VAL 209 A PRO 210 n 232 PRO 210 A ASP 211 n 233 ASP 211 A ALA 212 n 234 ALA 212 A LYS 213 n 235 LYS 213 A LEU 214 n 236 LEU 214 A ASP 215 n 237 ASP 215 A ASP 216 n 238 ASP 216 A GLY 217 n 239 GLY 217 A TYR 218 n 240 TYR 218 A PHE 219 n 241 PHE 219 A THR 220 n 242 THR 220 A LEU 221 n 243 LEU 221 A ILE 222 n 244 ILE 222 A ILE 223 n 245 ILE 223 A VAL 224 n 246 VAL 224 A GLU 225 n 247 GLU 225 A LYS 226 n 248 LYS 226 A SER 227 n 249 SER 227 A ASN 228 n 250 ASN 228 A LEU 229 n 251 LEU 229 A ALA 230 n 252 ALA 230 A GLU 231 n 253 GLU 231 A LEU 232 n 254 LEU 232 A GLY 233 n 255 GLY 233 A HIS 234 n 256 HIS 234 A ILE 235 n 257 ILE 235 A MSE 236 n 258 MSE 236 A THR 237 n 259 THR 237 A LEU 238 n 260 LEU 238 A ALA 239 n 261 ALA 239 A SER 240 n 262 SER 240 A ARG 241 n 263 ARG 241 A GLY 242 n 264 GLY 242 A GLU 243 n 265 GLU 243 A HIS 244 n 266 HIS 244 A THR 245 n 267 THR 245 A LYS 246 n 268 LYS 246 A HIS 247 n 269 HIS 247 A PRO 248 n 270 PRO 248 A LYS 249 n 271 LYS 249 A VAL 250 n 272 VAL 250 A ILE 251 n 273 ILE 251 A TYR 252 n 274 TYR 252 A GLU 253 n 275 GLU 253 A LYS 254 n 276 LYS 254 A ALA 255 n 277 ALA 255 A LYS 256 n 278 LYS 256 A ALA 257 n 279 ALA 257 A ILE 258 n 280 ILE 258 A ASN 259 n 281 ASN 259 A ILE 260 n 282 ILE 260 A SER 261 n 283 SER 261 A SER 262 n 284 SER 262 A PHE 263 n 285 PHE 263 A THR 264 n 286 THR 264 A ASP 265 n 287 ASP 265 A LEU 266 n 288 LEU 266 A ALA 267 n 289 GLN 267 A LEU 268 n 290 LEU 268 A ASN 269 n 291 ASN 269 A VAL 270 n 292 VAL 270 A ASP 271 n 293 ASP 271 A GLY 272 n 294 GLY 272 A GLU 273 n 295 GLU 273 A TYR 274 n 296 TYR 274 A GLY 275 n 297 GLY 275 A GLY 276 n 298 GLY 276 A LYS 277 n 299 LYS 277 A LEU 278 n 300 LEU 278 A PRO 279 n 301 PRO 279 A ALA 280 n 302 ALA 280 A ASN 281 n 303 ASN 281 A PHE 282 n 304 PHE 282 A LEU 283 n 305 LEU 283 A ASN 284 n 306 ASN 284 A LEU 285 n 307 LEU 285 A GLU 286 n 308 GLU 286 A ARG 287 n 309 ARG 287 A HIS 288 n 310 HIS 288 A ILE 289 n 311 ILE 289 A ASP 290 n 312 ASP 290 A VAL 291 n 313 VAL 291 A PHE 292 n 314 PHE 292 A ALA 293 n 315 ALA 293 A PRO 294 n 316 PRO 294 A ASN 295 n 317 ASN 295 A ASP 296 n 318 ASP 296 A ILE 297 n 319 ILE 297 A VAL 298 n 320 VAL 298 A ASN 299 n 321 ASN 299 A GLU 300 n 322 GLU 300 A GLU 301 n 323 GLU 301 A LEU 302 n 324 LEU 302 A ILE 303 n 325 ILE 303 A ASN 304 n 326 ASN 304 A ASN 305 n 327 ASN 305 A ASP 306 n 328 ASP 306 A HIS 307 n 329 HIS 307 A VAL 308 n 330 VAL 308 A ALA 309 n 331 ASP 309 A ALA 310 n 332 ASP 310 A ASN 311 n 333 ASN 311 A LEU 312 n 334 LEU 312 A n 335 313 A n 336 314 A n 337 315 A 2.0622 -1.7480 -0.2376 2.8803 0.1033 1.3444 0.1358 -0.0014 -0.0199 -0.0425 -0.0911 -0.0721 -0.0260 0.0218 -0.0447 -0.0960 -0.0286 -0.0305 -0.0549 0.0365 -0.1044 refined 57.3594 39.6975 21.3913 X-RAY DIFFRACTION 15.6810 -4.5680 7.4619 3.9168 -2.0515 9.4463 -0.2467 -0.6825 0.0752 0.3456 0.1075 -0.0115 -0.2163 1.0035 0.1392 -0.1061 0.0341 -0.0068 0.2071 0.0912 -0.0736 refined 81.3782 25.7499 32.2201 X-RAY DIFFRACTION 6.9970 -0.8824 0.6812 1.0319 0.1919 0.3777 -0.0669 -0.3633 -0.4159 -0.0507 -0.0118 0.0378 0.2378 0.0558 0.0787 -0.0420 0.0383 -0.0131 -0.0841 0.0724 -0.0819 refined 80.6206 19.0486 24.3563 X-RAY DIFFRACTION 7.3962 0.3019 1.1521 8.6303 -2.0601 6.0806 0.0492 0.3618 -0.1648 -0.2852 0.0725 0.2903 -0.1564 -0.0423 -0.1217 0.0080 0.0769 0.0515 -0.0552 0.0114 -0.1495 refined 91.7559 22.5470 17.5372 X-RAY DIFFRACTION 7.9025 -1.4924 0.3437 4.0166 0.4875 2.1110 -0.1975 -1.1044 -0.5486 0.3938 0.1936 0.0906 0.1500 0.0248 0.0040 -0.1043 0.0492 -0.0183 -0.0193 0.1247 -0.1161 refined 73.7884 19.2829 29.7515 X-RAY DIFFRACTION 10.3742 -4.1852 4.0752 17.2624 -5.9460 8.7137 0.5359 1.9443 -0.0013 -1.1273 -0.4027 -0.0158 0.0786 0.5026 -0.1331 0.0033 0.1568 -0.0567 0.1301 -0.0350 -0.2182 refined 64.0648 29.3605 3.5840 X-RAY DIFFRACTION A 1 A 124 X-RAY DIFFRACTION 1 A 135 A 144 X-RAY DIFFRACTION 2 A 166 A 200 X-RAY DIFFRACTION 3 A 207 A 229 X-RAY DIFFRACTION 3 A 230 A 249 X-RAY DIFFRACTION 4 A 250 A 286 X-RAY DIFFRACTION 5 A 296 A 312 X-RAY DIFFRACTION 6 software_defined_assembly PISA 1 monomeric author_defined_assembly 2 dimeric A LYS 213 A O LYS 235 1_555 A MG 501 B MG MG 1_555 A ASP 216 A OD2 ASP 238 1_555 84.6 A LYS 213 A O LYS 235 1_555 A MG 501 B MG MG 1_555 A TYR 218 A O TYR 240 1_555 171.4 A ASP 216 A OD2 ASP 238 1_555 A MG 501 B MG MG 1_555 A TYR 218 A O TYR 240 1_555 89.4 A LYS 213 A O LYS 235 1_555 A MG 501 B MG MG 1_555 A HOH 582 D O HOH 1_555 87.3 A ASP 216 A OD2 ASP 238 1_555 A MG 501 B MG MG 1_555 A HOH 582 D O HOH 1_555 83.8 A TYR 218 A O TYR 240 1_555 A MG 501 B MG MG 1_555 A HOH 582 D O HOH 1_555 98.1 A LYS 213 A O LYS 235 1_555 A MG 501 B MG MG 1_555 A HOH 531 D O HOH 1_555 90.9 A ASP 216 A OD2 ASP 238 1_555 A MG 501 B MG MG 1_555 A HOH 531 D O HOH 1_555 166.0 A TYR 218 A O TYR 240 1_555 A MG 501 B MG MG 1_555 A HOH 531 D O HOH 1_555 96.4 A HOH 582 D O HOH 1_555 A MG 501 B MG MG 1_555 A HOH 531 D O HOH 1_555 82.8 A LYS 213 A O LYS 235 1_555 A MG 501 B MG MG 1_555 A HOH 511 D O HOH 1_555 84.4 A ASP 216 A OD2 ASP 238 1_555 A MG 501 B MG MG 1_555 A HOH 511 D O HOH 1_555 98.7 A TYR 218 A O TYR 240 1_555 A MG 501 B MG MG 1_555 A HOH 511 D O HOH 1_555 90.5 A HOH 582 D O HOH 1_555 A MG 501 B MG MG 1_555 A HOH 511 D O HOH 1_555 171.0 A HOH 531 D O HOH 1_555 A MG 501 B MG MG 1_555 A HOH 511 D O HOH 1_555 94.0 A MSE 0 SELENOMETHIONINE A MSE 22 MET A MSE 1 SELENOMETHIONINE A MSE 23 MET A MSE 55 SELENOMETHIONINE A MSE 77 MET A MSE 92 SELENOMETHIONINE A MSE 114 MET A MSE 109 SELENOMETHIONINE A MSE 131 MET A MSE 128 SELENOMETHIONINE A MSE 150 MET A MSE 169 SELENOMETHIONINE A MSE 191 MET A MSE 173 SELENOMETHIONINE A MSE 195 MET A MSE 202 SELENOMETHIONINE A MSE 224 MET A MSE 236 SELENOMETHIONINE A MSE 258 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 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_556 y,x,-z+1 crystal symmetry operation 0.0000000000 0.0000000000 47.6800000000 A O GLU 35 A O GLU 57 A N LYS 3 A N LYS 25 A N ILE 8 A N ILE 30 A O ILE 63 A O ILE 85 A N ALA 64 A N ALA 86 A O GLY 88 A O GLY 110 A O ARG 131 A O ARG 153 A N MSE 128 A N MSE 150 A N THR 121 A N THR 143 A O VAL 291 A O VAL 313 A O PHE 282 A O PHE 304 A N ILE 258 A N ILE 280 A O ASN 259 A O ASN 281 A N GLU 181 A N GLU 203 A N ILE 180 A N ILE 202 A O PHE 187 A O PHE 209 A N GLY 197 A N GLY 219 A O THR 220 A O THR 242 A N ILE 223 A N ILE 245 A O ILE 251 A O ILE 273 A O ARG 131 A O ARG 153 A N MSE 128 A N MSE 150 A N THR 121 A N THR 143 A O VAL 291 A O VAL 313 A O PHE 282 A O PHE 304 A N ILE 258 A N ILE 280 A O ASN 259 A O ASN 281 A N GLU 181 A N GLU 203 A N ILE 180 A N ILE 202 A O PHE 187 A O PHE 209 A O LEU 196 A O LEU 218 A N ALA 137 A N ALA 159 A N ALA 138 A N ALA 160 A O ASN 269 A O ASN 291 A N VAL 270 A N VAL 292 A O GLU 273 A O GLU 295 1 A OG SER -2 A OG SER 20 1 Y 1 A CG HIS -1 A CG HIS 21 1 Y 1 A ND1 HIS -1 A ND1 HIS 21 1 Y 1 A CD2 HIS -1 A CD2 HIS 21 1 Y 1 A CE1 HIS -1 A CE1 HIS 21 1 Y 1 A NE2 HIS -1 A NE2 HIS 21 1 Y 1 A CG MSE 0 A CG MSE 22 1 Y 1 A SE MSE 0 A SE MSE 22 1 Y 1 A CE MSE 0 A CE MSE 22 1 Y 1 A CG GLN 144 A CG GLN 166 1 Y 1 A CD GLN 144 A CD GLN 166 1 Y 1 A OE1 GLN 144 A OE1 GLN 166 1 Y 1 A NE2 GLN 144 A NE2 GLN 166 1 Y 1 A CG TYR 162 A CG TYR 184 1 Y 1 A CD1 TYR 162 A CD1 TYR 184 1 Y 1 A CD2 TYR 162 A CD2 TYR 184 1 Y 1 A CE1 TYR 162 A CE1 TYR 184 1 Y 1 A CE2 TYR 162 A CE2 TYR 184 1 Y 1 A CZ TYR 162 A CZ TYR 184 1 Y 1 A OH TYR 162 A OH TYR 184 1 Y 1 A CG LYS 165 A CG LYS 187 1 Y 1 A CD LYS 165 A CD LYS 187 1 Y 1 A CE LYS 165 A CE LYS 187 1 Y 1 A NZ LYS 165 A NZ LYS 187 1 Y 1 A CG GLN 267 A CG GLN 289 1 Y 1 A CD GLN 267 A CD GLN 289 1 Y 1 A OE1 GLN 267 A OE1 GLN 289 1 Y 1 A NE2 GLN 267 A NE2 GLN 289 1 Y 1 A CG ASP 309 A CG ASP 331 1 Y 1 A OD1 ASP 309 A OD1 ASP 331 1 Y 1 A OD2 ASP 309 A OD2 ASP 331 1 Y 1 A CG ASP 310 A CG ASP 332 1 Y 1 A OD1 ASP 310 A OD1 ASP 332 1 Y 1 A OD2 ASP 310 A OD2 ASP 332 1 Y 1 A MSE -21 A MSE 1 1 Y 1 A GLY -20 A GLY 2 1 Y 1 A SER -19 A SER 3 1 Y 1 A SER -18 A SER 4 1 Y 1 A HIS -17 A HIS 5 1 Y 1 A HIS -16 A HIS 6 1 Y 1 A HIS -15 A HIS 7 1 Y 1 A HIS -14 A HIS 8 1 Y 1 A HIS -13 A HIS 9 1 Y 1 A HIS -12 A HIS 10 1 Y 1 A HIS -11 A HIS 11 1 Y 1 A SER -10 A SER 12 1 Y 1 A SER -9 A SER 13 1 Y 1 A GLY -8 A GLY 14 1 Y 1 A LEU -7 A LEU 15 1 Y 1 A VAL -6 A VAL 16 1 Y 1 A PRO -5 A PRO 17 1 Y 1 A ARG -4 A ARG 18 1 Y 1 A VAL 145 A VAL 167 1 Y 1 A SER 146 A SER 168 1 Y 1 A TYR 147 A TYR 169 1 Y 1 A GLU 148 A GLU 170 1 Y 1 A THR 149 A THR 171 1 Y 1 A PRO 150 A PRO 172 1 Y 1 A SER 151 A SER 173 1 Y 1 A LYS 152 A LYS 174 1 Y 1 A LEU 153 A LEU 175 1 Y 1 A LYS 154 A LYS 176 1 Y 1 A SER 155 A SER 177 1 Y 1 A ILE 156 A ILE 178 1 Y 1 A VAL 157 A VAL 179 1 Y 1 A ILE 313 A ILE 335 1 Y 1 A GLU 314 A GLU 336 1 Y 1 A GLU 315 A GLU 337 1 Y 1 A ASN 129 51.09 -105.56 1 A LYS 165 -102.04 78.99 1 A LEU 193 -170.82 144.32 1 A LEU 198 -106.12 -65.07 1 A MSE 202 -141.84 -155.23 34.138 0.00 0.00 0.00 0.00 0.00 -0.01 0.939 0.916 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 0.2464 0.20648 0.20845 2.30 29.17 857 16997 16069 5.1 99.58 10.497 0.156 RANDOM LIKELY RESIDUAL 1 THROUGHOUT Rigid body refinement of DgkB 0.312 0.228 0.80 0.80 1.20 MAXIMUM LIKELIHOOD MASK 2.30 29.17 152 2504 28 0 2324 0.007 0.022 2393 1.122 1.985 3240 5.887 5.000 301 39.929 25.093 108 14.053 15.000 406 17.523 15.000 11 0.061 0.200 363 0.003 0.020 1801 0.177 0.200 1050 0.300 0.200 1583 0.107 0.200 183 0.171 0.200 23 0.189 0.200 11 0.430 1.500 1542 0.676 2.000 2388 1.093 3.000 953 1.603 4.500 852 0.285 0.218 2.360 81 1130 20 99.34 2.3 30 2QV7 17025 16997 0 0 0.128 1 24.5 12.2 99.8 0.431 2.3 2.38 4.2 1667 1 8.3 99.8 refinement REFMAC 5.2.0005 data collection HKL-2000 data reduction HKL-2000 data scaling HKL-2000 phasing DgkB model used for rigid body refinement Diacylglycerol Kinase DgkB (E.C.2.7.1.107 ) Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg 1 N N 2 N N 3 N N 4 N N A GLN 17 A GLN 39 HELX_P A ALA 32 A ALA 54 1 1 16 A GLY 45 A GLY 67 HELX_P A MSE 55 A MSE 77 1 2 11 A GLY 67 A GLY 89 HELX_P A ALA 79 A ALA 101 1 3 13 A ASN 96 A ASN 118 HELX_P A LEU 102 A LEU 124 1 4 7 A ASP 107 A ASP 129 HELX_P A GLY 118 A GLY 140 1 5 12 A GLY 158 A GLY 180 HELX_P A TYR 162 A TYR 184 5 6 5 A MSE 169 A MSE 191 HELX_P A MSE 173 A MSE 195 5 7 5 A ASN 228 A ASN 250 HELX_P A SER 240 A SER 262 1 8 13 A ARG 241 A ARG 263 HELX_P A GLY 242 A GLY 264 5 9 2 A GLU 243 A GLU 265 HELX_P A HIS 247 A HIS 269 5 10 5 metalc 2.188 A LYS 213 A O LYS 235 1_555 A MG 501 B MG MG 1_555 metalc 2.338 A ASP 216 A OD2 ASP 238 1_555 A MG 501 B MG MG 1_555 metalc 2.239 A TYR 218 A O TYR 240 1_555 A MG 501 B MG MG 1_555 metalc 2.192 A MG 501 B MG MG 1_555 A HOH 582 D O HOH 1_555 metalc 2.381 A MG 501 B MG MG 1_555 A HOH 531 D O HOH 1_555 metalc 2.264 A MG 501 B MG MG 1_555 A HOH 511 D O HOH 1_555 covale 1.331 A HIS -1 A C HIS 21 1_555 A MSE 0 A N MSE 22 1_555 covale 1.331 A MSE 0 A C MSE 22 1_555 A MSE 1 A N MSE 23 1_555 covale 1.330 A MSE 1 A C MSE 23 1_555 A ARG 2 A N ARG 24 1_555 covale 1.334 A ALA 54 A C ALA 76 1_555 A MSE 55 A N MSE 77 1_555 covale 1.334 A MSE 55 A C MSE 77 1_555 A HIS 56 A N HIS 78 1_555 covale 1.329 A PRO 91 A C PRO 113 1_555 A MSE 92 A N MSE 114 1_555 covale 1.327 A MSE 92 A C MSE 114 1_555 A GLY 93 A N GLY 115 1_555 covale 1.329 A ILE 108 A C ILE 130 1_555 A MSE 109 A N MSE 131 1_555 covale 1.333 A MSE 109 A C MSE 131 1_555 A GLY 110 A N GLY 132 1_555 covale 1.329 A LYS 127 A C LYS 149 1_555 A MSE 128 A N MSE 150 1_555 covale 1.330 A MSE 128 A C MSE 150 1_555 A ASN 129 A N ASN 151 1_555 covale 1.334 A GLU 168 A C GLU 190 1_555 A MSE 169 A N MSE 191 1_555 covale 1.330 A MSE 169 A C MSE 191 1_555 A LEU 170 A N LEU 192 1_555 covale 1.329 A GLN 172 A C GLN 194 1_555 A MSE 173 A N MSE 195 1_555 covale 1.330 A MSE 173 A C MSE 195 1_555 A LYS 174 A N LYS 196 1_555 covale 1.329 A SER 201 A C SER 223 1_555 A MSE 202 A N MSE 224 1_555 covale 1.332 A MSE 202 A C MSE 224 1_555 A ALA 203 A N ALA 225 1_555 covale 1.332 A ILE 235 A C ILE 257 1_555 A MSE 236 A N MSE 258 1_555 covale 1.330 A MSE 236 A C MSE 258 1_555 A THR 237 A N THR 259 1_555 TRANSFERASE alpha-beta domain 1, beta sandwich domain 2, Protein-ADP complex, TRANSFERASE A LEU 278 A LEU 300 1 A PRO 279 A PRO 301 2.84 Q6GFF9_STAAR UNP 1 1 Q6GFF9 MRKRARIIYNPTSGKEQFKRELPDALIKLEKAGYETSAYATEKIGDATLEAERAMHENYDVLIAAGGDGTLNEVVNGIAE KPNRPKLGVIPMGTVNDFGRALHIPNDIMGALDVIIEGHSTKVDIGKMNNRYFINLAAGGQLTQVSYETPSKLKSIVGPF AYYIKGFEMLPQMKAVDLRIEYDGNVFQGEALLFFLGLTNSMAGFEKLVPDAKLDDGYFTLIIVEKSNLAELGHIMTLAS RGEHTKHPKVIYEKAKAINISSFTDLQLNVDGEYGGKLPANFLNLERHIDVFAPNDIVNEELINNDHVDDNLIEE 1 315 2QV7 1 315 Q6GFF9 A 1 23 337 1 EXPRESSION TAG MSE -21 2QV7 A Q6GFF9 UNP 1 1 EXPRESSION TAG GLY -20 2QV7 A Q6GFF9 UNP 2 1 EXPRESSION TAG SER -19 2QV7 A Q6GFF9 UNP 3 1 EXPRESSION TAG SER -18 2QV7 A Q6GFF9 UNP 4 1 EXPRESSION TAG HIS -17 2QV7 A Q6GFF9 UNP 5 1 EXPRESSION TAG HIS -16 2QV7 A Q6GFF9 UNP 6 1 EXPRESSION TAG HIS -15 2QV7 A Q6GFF9 UNP 7 1 EXPRESSION TAG HIS -14 2QV7 A Q6GFF9 UNP 8 1 EXPRESSION TAG HIS -13 2QV7 A Q6GFF9 UNP 9 1 EXPRESSION TAG HIS -12 2QV7 A Q6GFF9 UNP 10 1 EXPRESSION TAG HIS -11 2QV7 A Q6GFF9 UNP 11 1 EXPRESSION TAG SER -10 2QV7 A Q6GFF9 UNP 12 1 EXPRESSION TAG SER -9 2QV7 A Q6GFF9 UNP 13 1 EXPRESSION TAG GLY -8 2QV7 A Q6GFF9 UNP 14 1 EXPRESSION TAG LEU -7 2QV7 A Q6GFF9 UNP 15 1 EXPRESSION TAG VAL -6 2QV7 A Q6GFF9 UNP 16 1 EXPRESSION TAG PRO -5 2QV7 A Q6GFF9 UNP 17 1 EXPRESSION TAG ARG -4 2QV7 A Q6GFF9 UNP 18 1 EXPRESSION TAG GLY -3 2QV7 A Q6GFF9 UNP 19 1 EXPRESSION TAG SER -2 2QV7 A Q6GFF9 UNP 20 1 EXPRESSION TAG HIS -1 2QV7 A Q6GFF9 UNP 21 1 EXPRESSION TAG MSE 0 2QV7 A Q6GFF9 UNP 22 4 8 9 parallel parallel parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TYR 34 A TYR 56 A ALA 40 A ALA 62 A LYS 3 A LYS 25 A TYR 9 A TYR 31 A VAL 61 A VAL 83 A GLY 66 A GLY 88 A LYS 86 A LYS 108 A PRO 91 A PRO 113 A ARG 131 A ARG 153 A PHE 133 A PHE 155 A SER 120 A SER 142 A MSE 128 A MSE 150 A ALA 280 A ALA 302 A PHE 292 A PHE 314 A ALA 257 A ALA 279 A SER 261 A SER 283 A VAL 176 A VAL 198 A TYR 182 A TYR 204 A ASN 185 A ASN 207 A GLY 197 A GLY 219 A PHE 219 A PHE 241 A GLU 225 A GLU 247 A VAL 250 A VAL 272 A ALA 255 A ALA 277 A ARG 131 A ARG 153 A PHE 133 A PHE 155 A SER 120 A SER 142 A MSE 128 A MSE 150 A ALA 280 A ALA 302 A PHE 292 A PHE 314 A ALA 257 A ALA 279 A SER 261 A SER 283 A VAL 176 A VAL 198 A TYR 182 A TYR 204 A ASN 185 A ASN 207 A GLY 197 A GLY 219 A LEU 136 A LEU 158 A GLY 140 A GLY 162 A GLN 267 A GLN 289 A VAL 270 A VAL 292 A GLU 273 A GLU 295 A LYS 277 A LYS 299 BINDING SITE FOR RESIDUE MG A 501 Software 6 BINDING SITE FOR RESIDUE ADP A 500 Software 17 A LYS 213 A LYS 235 6 1_555 A ASP 216 A ASP 238 6 1_555 A TYR 218 A TYR 240 6 1_555 A HOH 511 D HOH 6 1_555 A HOH 531 D HOH 6 1_555 A HOH 582 D HOH 6 1_555 A ASN 10 A ASN 32 17 1_555 A THR 12 A THR 34 17 1_555 A SER 13 A SER 35 17 1_555 A GLY 14 A GLY 36 17 1_555 A THR 41 A THR 63 17 1_555 A GLU 42 A GLU 64 17 1_555 A LYS 43 A LYS 65 17 1_555 A ILE 44 A ILE 66 17 1_555 A GLY 66 A GLY 88 17 1_555 A GLY 67 A GLY 89 17 1_555 A GLY 69 A GLY 91 17 1_555 A THR 70 A THR 92 17 1_555 A GLU 73 A GLU 95 17 1_555 A GLY 93 A GLY 115 17 1_555 A THR 94 A THR 116 17 1_555 A HOH 527 D HOH 17 1_555 A HOH 625 D HOH 17 1_555 94 P 42 21 2