0.006549 0.003781 0.000000 0.000000 0.007562 0.000000 0.000000 0.000000 0.011547 0.00000 0.00000 0.00000 ATOMS WITH WEAK DENSITY HAVE BEEN REFINED WITH ZERO WEIGHT. LYS 272 IS COVALENTLY BOUND TO THE COFACTOR PLP. Hohenester, E. Jansonius, J.N. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 152.700 152.700 86.600 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 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 Li 1 6.941 LITHIUM ION non-polymer C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C6 H13 N O4 S 195.237 2-(N-MORPHOLINO)-ETHANESULFONIC ACID non-polymer C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Na 1 22.990 SODIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C8 H10 N O6 P 247.142 PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate non-polymer 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 US Biochemistry BICHAW 0033 0006-2960 33 13561 13570 10.1021/bi00250a008 7947767 An alkali metal ion size-dependent switch in the active site structure of dialkylglycine decarboxylase. 1994 US Science SCIEAS 0038 0036-8075 261 756 Dialkylglycine Decarboxylase Structure: Bifunctional Active Site and Alkali Metal Sites 1993 US J.Biol.Chem. JBCHA3 0071 0021-9258 265 5531 Pseudomonas Cepacia 2,2-Dialkylglycine Decarboxylase. Sequence and Expression in Escherichia Coli of Structural and Repressor Genes 1990 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 46374.145 DIALKYLGLYCINE DECARBOXYLASE 4.1.1.64 1 man polymer 22.990 SODIUM ION 1 syn non-polymer 6.941 LITHIUM ION 1 syn non-polymer 247.142 PYRIDOXAL-5'-PHOSPHATE 1 syn non-polymer 195.237 2-(N-MORPHOLINO)-ETHANESULFONIC ACID 1 syn non-polymer 18.015 water 99 nat water no no SLNDDATFWRNARHHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSG MLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAA VGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLI LDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVV QRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGM GGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL SLNDDATFWRNARHHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSG MLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAA VGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLI LDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVV QRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGM GGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 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 n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Burkholderia sample 292 Burkholderia cepacia 3.14 60.84 pdbx_database_status pdbx_unobs_or_zero_occ_atoms pdbx_unobs_or_zero_occ_residues struct_conf struct_conf_type repository Initial release Version format compliance Non-polymer description Version format compliance Advisory Derived calculations Other 1 0 1994-09-30 1 1 2008-03-03 1 2 2011-07-13 1 3 2017-11-29 _pdbx_database_status.process_site Y BNL 1994-06-29 REL NA SODIUM ION LI LITHIUM ION PLP PYRIDOXAL-5'-PHOSPHATE MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HOH water SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: DGDA_BURCE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 14 HIS 15 GLU 51 GLN 52 ILE 81 MET 82 VAL 82 LEU 83 ARG 307 PRO 308 PRO 309 LEU 309 GLY 312 ALA 312 THE PUBLISHED AMINO ACID SEQUENCE (REFERENCE 1) WAS CORRECTED AT THREE POSITIONS. RESEQUENCING OF SEVERAL GC-RICH REGIONS OF THE DGDA GENE VERIFIED THESE CHANGES (J.W. KELLER, PERSONAL COMMUNICATION): GLU 52 --> GLN 52 ILE 82, VAL 83 --> MET 82, LEU 83 ARG 308, CYS 309, PRO 310, PRO 311, ALA 312, GLY 313 --> PRO 308, LEU 309, PRO 310, ALA 311, ALA 312 (INCLUDES A DELETION). GLN 15 -->HIS 15 (M.D. TONEY ET AL., J. MOL. BIOL. 222: 873-875 (1991)). NA 435 2 NA NA 435 A LI 436 3 LI LI 436 A PLP 272 4 PLP PLP 437 A MES 434 5 MES MES 434 A HOH 501 6 HOH HOH 501 A HOH 502 6 HOH HOH 502 A HOH 503 6 HOH HOH 503 A HOH 504 6 HOH HOH 504 A HOH 505 6 HOH HOH 505 A HOH 506 6 HOH HOH 506 A HOH 507 6 HOH HOH 507 A HOH 508 6 HOH HOH 508 A HOH 509 6 HOH HOH 509 A HOH 510 6 HOH HOH 510 A HOH 511 6 HOH HOH 511 A HOH 512 6 HOH HOH 512 A HOH 513 6 HOH HOH 513 A HOH 514 6 HOH HOH 514 A HOH 515 6 HOH HOH 515 A HOH 516 6 HOH HOH 516 A HOH 517 6 HOH HOH 517 A HOH 518 6 HOH HOH 518 A HOH 519 6 HOH HOH 519 A HOH 520 6 HOH HOH 520 A HOH 521 6 HOH HOH 521 A HOH 522 6 HOH HOH 522 A HOH 523 6 HOH HOH 523 A HOH 524 6 HOH HOH 524 A HOH 525 6 HOH HOH 525 A HOH 526 6 HOH HOH 526 A HOH 527 6 HOH HOH 527 A HOH 528 6 HOH HOH 528 A HOH 529 6 HOH HOH 529 A HOH 530 6 HOH HOH 530 A HOH 531 6 HOH HOH 531 A HOH 532 6 HOH HOH 532 A HOH 533 6 HOH HOH 533 A HOH 534 6 HOH HOH 534 A HOH 535 6 HOH HOH 535 A HOH 536 6 HOH HOH 536 A HOH 537 6 HOH HOH 537 A HOH 538 6 HOH HOH 538 A HOH 539 6 HOH HOH 539 A HOH 540 6 HOH HOH 540 A HOH 541 6 HOH HOH 541 A HOH 542 6 HOH HOH 542 A HOH 543 6 HOH HOH 543 A HOH 544 6 HOH HOH 544 A HOH 545 6 HOH HOH 545 A HOH 546 6 HOH HOH 546 A HOH 547 6 HOH HOH 547 A HOH 548 6 HOH HOH 548 A HOH 549 6 HOH HOH 549 A HOH 550 6 HOH HOH 550 A HOH 551 6 HOH HOH 551 A HOH 552 6 HOH HOH 552 A HOH 553 6 HOH HOH 553 A HOH 554 6 HOH HOH 554 A HOH 555 6 HOH HOH 555 A HOH 556 6 HOH HOH 556 A HOH 557 6 HOH HOH 557 A HOH 558 6 HOH HOH 558 A HOH 559 6 HOH HOH 559 A HOH 560 6 HOH HOH 560 A HOH 561 6 HOH HOH 561 A HOH 562 6 HOH HOH 562 A HOH 563 6 HOH HOH 563 A HOH 564 6 HOH HOH 564 A HOH 565 6 HOH HOH 565 A HOH 566 6 HOH HOH 566 A HOH 567 6 HOH HOH 567 A HOH 568 6 HOH HOH 568 A HOH 569 6 HOH HOH 569 A HOH 570 6 HOH HOH 570 A HOH 571 6 HOH HOH 571 A HOH 572 6 HOH HOH 572 A HOH 573 6 HOH HOH 573 A HOH 574 6 HOH HOH 574 A HOH 575 6 HOH HOH 575 A HOH 576 6 HOH HOH 576 A HOH 577 6 HOH HOH 577 A HOH 578 6 HOH HOH 578 A HOH 579 6 HOH HOH 579 A HOH 580 6 HOH HOH 580 A HOH 581 6 HOH HOH 581 A HOH 582 6 HOH HOH 582 A HOH 583 6 HOH HOH 583 A HOH 584 6 HOH HOH 584 A HOH 585 6 HOH HOH 585 A HOH 586 6 HOH HOH 586 A HOH 587 6 HOH HOH 587 A HOH 588 6 HOH HOH 588 A HOH 589 6 HOH HOH 589 A HOH 590 6 HOH HOH 590 A HOH 591 6 HOH HOH 591 A HOH 592 6 HOH HOH 592 A HOH 593 6 HOH HOH 593 A HOH 594 6 HOH HOH 594 A HOH 595 6 HOH HOH 595 A HOH 596 6 HOH HOH 596 A HOH 597 6 HOH HOH 597 A HOH 598 6 HOH HOH 598 A HOH 599 6 HOH HOH 599 A n 1 2 A LEU 3 n 2 LEU 3 A ASN 4 n 3 ASN 4 A ASP 5 n 4 ASP 5 A ASP 6 n 5 ASP 6 A ALA 7 n 6 ALA 7 A THR 8 n 7 THR 8 A PHE 9 n 8 PHE 9 A TRP 10 n 9 TRP 10 A ARG 11 n 10 ARG 11 A ASN 12 n 11 ASN 12 A ALA 13 n 12 ALA 13 A ARG 14 n 13 ARG 14 A HIS 15 n 14 HIS 15 A HIS 16 n 15 HIS 16 A LEU 17 n 16 LEU 17 A VAL 18 n 17 VAL 18 A ARG 19 n 18 ARG 19 A TYR 20 n 19 TYR 20 A GLY 21 n 20 GLY 21 A GLY 22 n 21 GLY 22 A THR 23 n 22 THR 23 A PHE 24 n 23 PHE 24 A GLU 25 n 24 GLU 25 A PRO 26 n 25 PRO 26 A MET 27 n 26 MET 27 A ILE 28 n 27 ILE 28 A ILE 29 n 28 ILE 29 A GLU 30 n 29 GLU 30 A ARG 31 n 30 ARG 31 A ALA 32 n 31 ALA 32 A LYS 33 n 32 LYS 33 A GLY 34 n 33 GLY 34 A SER 35 n 34 SER 35 A PHE 36 n 35 PHE 36 A VAL 37 n 36 VAL 37 A TYR 38 n 37 TYR 38 A ASP 39 n 38 ASP 39 A ALA 40 n 39 ALA 40 A ASP 41 n 40 ASP 41 A GLY 42 n 41 GLY 42 A ARG 43 n 42 ARG 43 A ALA 44 n 43 ALA 44 A ILE 45 n 44 ILE 45 A LEU 46 n 45 LEU 46 A ASP 47 n 46 ASP 47 A PHE 48 n 47 PHE 48 A THR 49 n 48 THR 49 A SER 50 n 49 SER 50 A GLY 51 n 50 GLY 51 A GLN 52 n 51 GLN 52 A MET 53 n 52 MET 53 A SER 54 n 53 SER 54 A ALA 55 n 54 ALA 55 A VAL 56 n 55 VAL 56 A LEU 57 n 56 LEU 57 A GLY 58 n 57 GLY 58 A HIS 59 n 58 HIS 59 A CYS 60 n 59 CYS 60 A HIS 61 n 60 HIS 61 A PRO 62 n 61 PRO 62 A GLU 63 n 62 GLU 63 A ILE 64 n 63 ILE 64 A VAL 65 n 64 VAL 65 A SER 66 n 65 SER 66 A VAL 67 n 66 VAL 67 A ILE 68 n 67 ILE 68 A GLY 69 n 68 GLY 69 A GLU 70 n 69 GLU 70 A TYR 71 n 70 TYR 71 A ALA 72 n 71 ALA 72 A GLY 73 n 72 GLY 73 A LYS 74 n 73 LYS 74 A LEU 75 n 74 LEU 75 A ASP 76 n 75 ASP 76 A HIS 77 n 76 HIS 77 A LEU 78 n 77 LEU 78 A PHE 79 n 78 PHE 79 A SER 80 n 79 SER 80 A GLY 81 n 80 GLY 81 A MET 82 n 81 MET 82 A LEU 83 n 82 LEU 83 A SER 84 n 83 SER 84 A ARG 85 n 84 ARG 85 A PRO 86 n 85 PRO 86 A VAL 87 n 86 VAL 87 A VAL 88 n 87 VAL 88 A ASP 89 n 88 ASP 89 A LEU 90 n 89 LEU 90 A ALA 91 n 90 ALA 91 A THR 92 n 91 THR 92 A ARG 93 n 92 ARG 93 A LEU 94 n 93 LEU 94 A ALA 95 n 94 ALA 95 A ASN 96 n 95 ASN 96 A ILE 97 n 96 ILE 97 A THR 98 n 97 THR 98 A PRO 99 n 98 PRO 99 A PRO 100 n 99 PRO 100 A GLY 101 n 100 GLY 101 A LEU 102 n 101 LEU 102 A ASP 103 n 102 ASP 103 A ARG 104 n 103 ARG 104 A ALA 105 n 104 ALA 105 A LEU 106 n 105 LEU 106 A LEU 107 n 106 LEU 107 A LEU 108 n 107 LEU 108 A SER 109 n 108 SER 109 A THR 110 n 109 THR 110 A GLY 111 n 110 GLY 111 A ALA 112 n 111 ALA 112 A GLU 113 n 112 GLU 113 A SER 114 n 113 SER 114 A ASN 115 n 114 ASN 115 A GLU 116 n 115 GLU 116 A ALA 117 n 116 ALA 117 A ALA 118 n 117 ALA 118 A ILE 119 n 118 ILE 119 A ARG 120 n 119 ARG 120 A MET 121 n 120 MET 121 A ALA 122 n 121 ALA 122 A LYS 123 n 122 LYS 123 A LEU 124 n 123 LEU 124 A VAL 125 n 124 VAL 125 A THR 126 n 125 THR 126 A GLY 127 n 126 GLY 127 A LYS 128 n 127 LYS 128 A TYR 129 n 128 TYR 129 A GLU 130 n 129 GLU 130 A ILE 131 n 130 ILE 131 A VAL 132 n 131 VAL 132 A GLY 133 n 132 GLY 133 A PHE 134 n 133 PHE 134 A ALA 135 n 134 ALA 135 A GLN 136 n 135 GLN 136 A SER 137 n 136 SER 137 A TRP 138 n 137 TRP 138 A HIS 139 n 138 HIS 139 A GLY 140 n 139 GLY 140 A MET 141 n 140 MET 141 A THR 142 n 141 THR 142 A GLY 143 n 142 GLY 143 A ALA 144 n 143 ALA 144 A ALA 145 n 144 ALA 145 A ALA 146 n 145 ALA 146 A SER 147 n 146 SER 147 A ALA 148 n 147 ALA 148 A THR 149 n 148 THR 149 A TYR 150 n 149 TYR 150 A SER 151 n 150 SER 151 A ALA 152 n 151 ALA 152 A GLY 153 n 152 GLY 153 A ARG 154 n 153 ARG 154 A LYS 155 n 154 LYS 155 A GLY 156 n 155 GLY 156 A VAL 157 n 156 VAL 157 A GLY 158 n 157 GLY 158 A PRO 159 n 158 PRO 159 A ALA 160 n 159 ALA 160 A ALA 161 n 160 ALA 161 A VAL 162 n 161 VAL 162 A GLY 163 n 162 GLY 163 A SER 164 n 163 SER 164 A PHE 165 n 164 PHE 165 A ALA 166 n 165 ALA 166 A ILE 167 n 166 ILE 167 A PRO 168 n 167 PRO 168 A ALA 169 n 168 ALA 169 A PRO 170 n 169 PRO 170 A PHE 171 n 170 PHE 171 A THR 172 n 171 THR 172 A TYR 173 n 172 TYR 173 A ARG 174 n 173 ARG 174 A PRO 175 n 174 PRO 175 A ARG 176 n 175 ARG 176 A PHE 177 n 176 PHE 177 A GLU 178 n 177 GLU 178 A ARG 179 n 178 ARG 179 A ASN 180 n 179 ASN 180 A GLY 181 n 180 GLY 181 A ALA 182 n 181 ALA 182 A TYR 183 n 182 TYR 183 A ASP 184 n 183 ASP 184 A TYR 185 n 184 TYR 185 A LEU 186 n 185 LEU 186 A ALA 187 n 186 ALA 187 A GLU 188 n 187 GLU 188 A LEU 189 n 188 LEU 189 A ASP 190 n 189 ASP 190 A TYR 191 n 190 TYR 191 A ALA 192 n 191 ALA 192 A PHE 193 n 192 PHE 193 A ASP 194 n 193 ASP 194 A LEU 195 n 194 LEU 195 A ILE 196 n 195 ILE 196 A ASP 197 n 196 ASP 197 A ARG 198 n 197 ARG 198 A GLN 199 n 198 GLN 199 A SER 200 n 199 SER 200 A SER 201 n 200 SER 201 A GLY 202 n 201 GLY 202 A ASN 203 n 202 ASN 203 A LEU 204 n 203 LEU 204 A ALA 205 n 204 ALA 205 A ALA 206 n 205 ALA 206 A PHE 207 n 206 PHE 207 A ILE 208 n 207 ILE 208 A ALA 209 n 208 ALA 209 A GLU 210 n 209 GLU 210 A PRO 211 n 210 PRO 211 A ILE 212 n 211 ILE 212 A LEU 213 n 212 LEU 213 A SER 214 n 213 SER 214 A SER 215 n 214 SER 215 A GLY 216 n 215 GLY 216 A GLY 217 n 216 GLY 217 A ILE 218 n 217 ILE 218 A ILE 219 n 218 ILE 219 A GLU 220 n 219 GLU 220 A LEU 221 n 220 LEU 221 A PRO 222 n 221 PRO 222 A ASP 223 n 222 ASP 223 A GLY 224 n 223 GLY 224 A TYR 225 n 224 TYR 225 A MET 226 n 225 MET 226 A ALA 227 n 226 ALA 227 A ALA 228 n 227 ALA 228 A LEU 229 n 228 LEU 229 A LYS 230 n 229 LYS 230 A ARG 231 n 230 ARG 231 A LYS 232 n 231 LYS 232 A CYS 233 n 232 CYS 233 A GLU 234 n 233 GLU 234 A ALA 235 n 234 ALA 235 A ARG 236 n 235 ARG 236 A GLY 237 n 236 GLY 237 A MET 238 n 237 MET 238 A LEU 239 n 238 LEU 239 A LEU 240 n 239 LEU 240 A ILE 241 n 240 ILE 241 A LEU 242 n 241 LEU 242 A ASP 243 n 242 ASP 243 A GLU 244 n 243 GLU 244 A ALA 245 n 244 ALA 245 A GLN 246 n 245 GLN 246 A THR 247 n 246 THR 247 A GLY 248 n 247 GLY 248 A VAL 249 n 248 VAL 249 A GLY 250 n 249 GLY 250 A ARG 251 n 250 ARG 251 A THR 252 n 251 THR 252 A GLY 253 n 252 GLY 253 A THR 254 n 253 THR 254 A MET 255 n 254 MET 255 A PHE 256 n 255 PHE 256 A ALA 257 n 256 ALA 257 A CYS 258 n 257 CYS 258 A GLN 259 n 258 GLN 259 A ARG 260 n 259 ARG 260 A ASP 261 n 260 ASP 261 A GLY 262 n 261 GLY 262 A VAL 263 n 262 VAL 263 A THR 264 n 263 THR 264 A PRO 265 n 264 PRO 265 A ASP 266 n 265 ASP 266 A ILE 267 n 266 ILE 267 A LEU 268 n 267 LEU 268 A THR 269 n 268 THR 269 A LEU 270 n 269 LEU 270 A SER 271 n 270 SER 271 A LYS 272 n 271 LYS 272 A THR 273 n 272 THR 273 A LEU 274 n 273 LEU 274 A GLY 275 n 274 GLY 275 A ALA 276 n 275 ALA 276 A GLY 277 n 276 GLY 277 A LEU 278 n 277 LEU 278 A PRO 279 n 278 PRO 279 A LEU 280 n 279 LEU 280 A ALA 281 n 280 ALA 281 A ALA 282 n 281 ALA 282 A ILE 283 n 282 ILE 283 A VAL 284 n 283 VAL 284 A THR 285 n 284 THR 285 A SER 286 n 285 SER 286 A ALA 287 n 286 ALA 287 A ALA 288 n 287 ALA 288 A ILE 289 n 288 ILE 289 A GLU 290 n 289 GLU 290 A GLU 291 n 290 GLU 291 A ARG 292 n 291 ARG 292 A ALA 293 n 292 ALA 293 A HIS 294 n 293 HIS 294 A GLU 295 n 294 GLU 295 A LEU 296 n 295 LEU 296 A GLY 297 n 296 GLY 297 A TYR 298 n 297 TYR 298 A LEU 299 n 298 LEU 299 A PHE 300 n 299 PHE 300 A TYR 301 n 300 TYR 301 A THR 302 n 301 THR 302 A THR 303 n 302 THR 303 A HIS 304 n 303 HIS 304 A VAL 305 n 304 VAL 305 A SER 306 n 305 SER 306 A ASP 307 n 306 ASP 307 A PRO 308 n 307 PRO 308 A LEU 309 n 308 LEU 309 A PRO 310 n 309 PRO 310 A ALA 311 n 310 ALA 311 A ALA 312 n 311 ALA 312 A VAL 313 n 312 VAL 313 A GLY 314 n 313 GLY 314 A LEU 315 n 314 LEU 315 A ARG 316 n 315 ARG 316 A VAL 317 n 316 VAL 317 A LEU 318 n 317 LEU 318 A ASP 319 n 318 ASP 319 A VAL 320 n 319 VAL 320 A VAL 321 n 320 VAL 321 A GLN 322 n 321 GLN 322 A ARG 323 n 322 ARG 323 A ASP 324 n 323 ASP 324 A GLY 325 n 324 GLY 325 A LEU 326 n 325 LEU 326 A VAL 327 n 326 VAL 327 A ALA 328 n 327 ALA 328 A ARG 329 n 328 ARG 329 A ALA 330 n 329 ALA 330 A ASN 331 n 330 ASN 331 A VAL 332 n 331 VAL 332 A MET 333 n 332 MET 333 A GLY 334 n 333 GLY 334 A ASP 335 n 334 ASP 335 A ARG 336 n 335 ARG 336 A LEU 337 n 336 LEU 337 A ARG 338 n 337 ARG 338 A ARG 339 n 338 ARG 339 A GLY 340 n 339 GLY 340 A LEU 341 n 340 LEU 341 A LEU 342 n 341 LEU 342 A ASP 343 n 342 ASP 343 A LEU 344 n 343 LEU 344 A MET 345 n 344 MET 345 A GLU 346 n 345 GLU 346 A ARG 347 n 346 ARG 347 A PHE 348 n 347 PHE 348 A ASP 349 n 348 ASP 349 A CYS 350 n 349 CYS 350 A ILE 351 n 350 ILE 351 A GLY 352 n 351 GLY 352 A ASP 353 n 352 ASP 353 A VAL 354 n 353 VAL 354 A ARG 355 n 354 ARG 355 A GLY 356 n 355 GLY 356 A ARG 357 n 356 ARG 357 A GLY 358 n 357 GLY 358 A LEU 359 n 358 LEU 359 A LEU 360 n 359 LEU 360 A LEU 361 n 360 LEU 361 A GLY 362 n 361 GLY 362 A VAL 363 n 362 VAL 363 A GLU 364 n 363 GLU 364 A ILE 365 n 364 ILE 365 A VAL 366 n 365 VAL 366 A LYS 367 n 366 LYS 367 A ASP 368 n 367 ASP 368 A ARG 369 n 368 ARG 369 A ARG 370 n 369 ARG 370 A THR 371 n 370 THR 371 A LYS 372 n 371 LYS 372 A GLU 373 n 372 GLU 373 A PRO 374 n 373 PRO 374 A ALA 375 n 374 ALA 375 A ASP 376 n 375 ASP 376 A GLY 377 n 376 GLY 377 A LEU 378 n 377 LEU 378 A GLY 379 n 378 GLY 379 A ALA 380 n 379 ALA 380 A LYS 381 n 380 LYS 381 A ILE 382 n 381 ILE 382 A THR 383 n 382 THR 383 A ARG 384 n 383 ARG 384 A GLU 385 n 384 GLU 385 A CYS 386 n 385 CYS 386 A MET 387 n 386 MET 387 A ASN 388 n 387 ASN 388 A LEU 389 n 388 LEU 389 A GLY 390 n 389 GLY 390 A LEU 391 n 390 LEU 391 A SER 392 n 391 SER 392 A MET 393 n 392 MET 393 A ASN 394 n 393 ASN 394 A ILE 395 n 394 ILE 395 A VAL 396 n 395 VAL 396 A GLN 397 n 396 GLN 397 A LEU 398 n 397 LEU 398 A PRO 399 n 398 PRO 399 A GLY 400 n 399 GLY 400 A MET 401 n 400 MET 401 A GLY 402 n 401 GLY 402 A GLY 403 n 402 GLY 403 A VAL 404 n 403 VAL 404 A PHE 405 n 404 PHE 405 A ARG 406 n 405 ARG 406 A ILE 407 n 406 ILE 407 A ALA 408 n 407 ALA 408 A PRO 409 n 408 PRO 409 A PRO 410 n 409 PRO 410 A LEU 411 n 410 LEU 411 A THR 412 n 411 THR 412 A VAL 413 n 412 VAL 413 A SER 414 n 413 SER 414 A GLU 415 n 414 GLU 415 A ASP 416 n 415 ASP 416 A GLU 417 n 416 GLU 417 A ILE 418 n 417 ILE 418 A ASP 419 n 418 ASP 419 A LEU 420 n 419 LEU 420 A GLY 421 n 420 GLY 421 A LEU 422 n 421 LEU 422 A SER 423 n 422 SER 423 A LEU 424 n 423 LEU 424 A LEU 425 n 424 LEU 425 A GLY 426 n 425 GLY 426 A GLN 427 n 426 GLN 427 A ALA 428 n 427 ALA 428 A ILE 429 n 428 ILE 429 A GLU 430 n 429 GLU 430 A ARG 431 n 430 ARG 431 A ALA 432 n 431 ALA 432 A LEU 433 n 432 LEU 433 A author_defined_assembly 4 tetrameric A ALA 95 A O ALA 94 1_555 A NA 435 B NA NA 1_555 A LEU 102 A O LEU 101 1_555 91.8 A ALA 95 A O ALA 94 1_555 A NA 435 B NA NA 1_555 A HOH 540 F O HOH 1_555 90.8 A LEU 102 A O LEU 101 1_555 A NA 435 B NA NA 1_555 A HOH 540 F O HOH 1_555 85.3 A ALA 95 A O ALA 94 1_555 A NA 435 B NA NA 1_555 A PRO 99 A O PRO 98 1_555 165.7 A LEU 102 A O LEU 101 1_555 A NA 435 B NA NA 1_555 A PRO 99 A O PRO 98 1_555 101.3 A HOH 540 F O HOH 1_555 A NA 435 B NA NA 1_555 A PRO 99 A O PRO 98 1_555 95.9 A ALA 95 A O ALA 94 1_555 A NA 435 B NA NA 1_555 A THR 98 A O THR 97 1_555 90.1 A LEU 102 A O LEU 101 1_555 A NA 435 B NA NA 1_555 A THR 98 A O THR 97 1_555 156.5 A HOH 540 F O HOH 1_555 A NA 435 B NA NA 1_555 A THR 98 A O THR 97 1_555 118.0 A PRO 99 A O PRO 98 1_555 A NA 435 B NA NA 1_555 A THR 98 A O THR 97 1_555 75.7 A ALA 95 A O ALA 94 1_555 A NA 435 B NA NA 1_555 A THR 98 A OG1 THR 97 1_555 71.6 A LEU 102 A O LEU 101 1_555 A NA 435 B NA NA 1_555 A THR 98 A OG1 THR 97 1_555 84.6 A HOH 540 F O HOH 1_555 A NA 435 B NA NA 1_555 A THR 98 A OG1 THR 97 1_555 159.4 A PRO 99 A O PRO 98 1_555 A NA 435 B NA NA 1_555 A THR 98 A OG1 THR 97 1_555 103.7 A THR 98 A O THR 97 1_555 A NA 435 B NA NA 1_555 A THR 98 A OG1 THR 97 1_555 73.8 A HOH 552 F O HOH 1_555 A LI 436 C LI LI 1_555 A LEU 78 A O LEU 77 1_555 96.5 A HOH 552 F O HOH 1_555 A LI 436 C LI LI 1_555 A HOH 539 F O HOH 1_555 112.9 A LEU 78 A O LEU 77 1_555 A LI 436 C LI LI 1_555 A HOH 539 F O HOH 1_555 96.5 A HOH 552 F O HOH 1_555 A LI 436 C LI LI 1_555 A ASP 307 A OD1 ASP 306 1_555 128.2 A LEU 78 A O LEU 77 1_555 A LI 436 C LI LI 1_555 A ASP 307 A OD1 ASP 306 1_555 118.9 A HOH 539 F O HOH 1_555 A LI 436 C LI LI 1_555 A ASP 307 A OD1 ASP 306 1_555 100.0 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 -0.5000000000 0.8660254038 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 7_555 y,x,-z+1/3 crystal symmetry operation 0.0000000000 0.0000000000 28.8666666667 0.5000000000 -0.8660254038 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 10_665 -y+1,-x+1,-z+1/3 crystal symmetry operation 76.3500000000 132.2420791579 28.8666666667 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4_665 -x+1,-y+1,z crystal symmetry operation 76.3500000000 132.2420791579 0.0000000000 A O LYS 33 A O LYS 32 A N TYR 38 A N TYR 37 A O VAL 37 A O VAL 36 A N ILE 45 A N ILE 44 A N ARG 104 A N ARG 103 A O THR 285 A O THR 284 A O VAL 284 A O VAL 283 A N LEU 268 A N LEU 267 A O ILE 267 A O ILE 266 A N LEU 242 A N LEU 241 A O ILE 241 A O ILE 240 A N ALA 209 A N ALA 208 A N ILE 208 A N ILE 207 A O VAL 132 A O VAL 131 A N GLY 133 A N GLY 132 A O PHE 165 A O PHE 164 1 A SER 2 A SER 1 1 Y 1 -4.45 0.50 120.30 115.85 A A A NE CZ NH1 ARG ARG ARG 19 19 19 N 1 -6.24 0.90 118.30 112.06 A A A CB CG OD2 ASP ASP ASP 41 41 41 N 1 -7.08 0.90 118.30 111.22 A A A CB CG OD1 ASP ASP ASP 47 47 47 N 1 5.86 0.90 118.30 124.16 A A A CB CG OD2 ASP ASP ASP 47 47 47 N 1 5.63 0.90 118.30 123.93 A A A CB CG OD1 ASP ASP ASP 89 89 89 N 1 -7.12 0.90 118.30 111.18 A A A CB CG OD2 ASP ASP ASP 89 89 89 N 1 -3.94 0.50 120.30 116.36 A A A NE CZ NH2 ARG ARG ARG 93 93 93 N 1 -5.91 0.90 118.30 112.39 A A A CB CG OD2 ASP ASP ASP 103 103 103 N 1 -3.10 0.50 120.30 117.20 A A A NE CZ NH1 ARG ARG ARG 120 120 120 N 1 -15.75 2.10 128.40 112.65 A A A C N CD ARG PRO PRO 174 175 175 Y 1 -5.83 0.90 118.30 112.47 A A A CB CG OD2 ASP ASP ASP 184 184 184 N 1 5.57 0.90 118.30 123.87 A A A CB CG OD1 ASP ASP ASP 190 190 190 N 1 -7.94 0.90 118.30 110.36 A A A CB CG OD2 ASP ASP ASP 190 190 190 N 1 5.94 0.90 118.30 124.24 A A A CB CG OD1 ASP ASP ASP 197 197 197 N 1 -6.10 0.90 118.30 112.20 A A A CB CG OD1 ASP ASP ASP 223 223 223 N 1 -13.69 1.70 113.30 99.61 A A A CA CB CG MET MET MET 226 226 226 N 1 6.91 0.90 118.30 125.21 A A A CB CG OD1 ASP ASP ASP 307 307 307 N 1 -7.12 0.90 118.30 111.18 A A A CB CG OD2 ASP ASP ASP 307 307 307 N 1 -6.12 0.90 118.30 112.18 A A A CB CG OD2 ASP ASP ASP 319 319 319 N 1 3.90 0.50 120.30 124.20 A A A NE CZ NH1 ARG ARG ARG 323 323 323 N 1 -5.26 0.50 120.30 115.04 A A A NE CZ NH2 ARG ARG ARG 323 323 323 N 1 -5.90 0.90 118.30 112.40 A A A CB CG OD2 ASP ASP ASP 324 324 324 N 1 7.07 0.90 118.30 125.37 A A A CB CG OD1 ASP ASP ASP 343 343 343 N 1 -6.76 0.90 118.30 111.54 A A A CB CG OD2 ASP ASP ASP 343 343 343 N 1 -6.65 0.90 118.30 111.65 A A A CB CG OD1 ASP ASP ASP 349 349 349 N 1 -6.63 0.90 118.30 111.67 A A A CB CG OD1 ASP ASP ASP 368 368 368 N 1 5.86 0.90 118.30 124.16 A A A CB CG OD2 ASP ASP ASP 368 368 368 N 1 6.67 0.90 118.30 124.97 A A A CB CG OD1 ASP ASP ASP 419 419 419 N 1 -6.41 0.90 118.30 111.89 A A A CB CG OD2 ASP ASP ASP 419 419 419 N 1 A A CD OE2 GLU GLU 30 30 0.068 0.011 1.252 1.320 N 1 A A CD OE2 GLU GLU 63 63 0.069 0.011 1.252 1.321 N 1 A A CD OE2 GLU GLU 70 70 0.081 0.011 1.252 1.333 N 1 A A CD OE1 GLU GLU 113 113 0.073 0.011 1.252 1.325 N 1 A A CD OE1 GLU GLU 116 116 0.091 0.011 1.252 1.343 N 1 A A CD OE2 GLU GLU 178 178 0.099 0.011 1.252 1.351 N 1 A A CD OE1 GLU GLU 220 220 0.088 0.011 1.252 1.340 N 1 A A CD OE1 GLU GLU 291 291 0.077 0.011 1.252 1.329 N 1 A A CD OE1 GLU GLU 385 385 0.085 0.011 1.252 1.337 N 1 A A CD OE1 GLU GLU 415 415 0.079 0.011 1.252 1.331 N 1 A ASP 5 -92.09 47.06 1 A PRO 26 -90.78 47.16 1 A GLN 52 -96.69 59.58 1 A ALA 55 -52.91 61.16 1 A LEU 108 -119.62 -157.28 1 A SER 271 -167.00 -80.63 1 A PHE 300 -153.03 88.15 1 A LEU 359 -107.77 41.58 1 A ALA 408 -166.36 77.46 0.1780000 2.8 8. 14224 1 0.0 2.8 8. 99 3375 29 0 3247 0.012 2.6 0.009 1.7 refinement TNT DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE) (DGD) (E.C.4.1.1.64) MUTANT WITH GLN 15 REPLACED BY HIS (Q15H) COMPLEXED WITH LITHIUM+ IN METAL-BINDING SITE 1 AN ALKALI METAL ION SIZE-DEPENDENT SWITCH IN THE ACTIVE SITE STRUCTURE OF DIALKYLGLYCINE DECARBOXYLASE 1 N N 2 N N 3 N N 4 N N 5 N N 6 N N THE MOLECULE IS A TETRAMER OF IDENTICAL SUBUNITS. THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH COMPRISES ONE MONOMER. THE TETRAMER CAN BE GENERATED BY CRYSTALLOGRAPHIC DYADS. APPLYING THE FOLLOWING TRANSFORMATION TO THE COORDINATES IN THIS ENTRY WILL YIELD A DIMER: MTRIX1 1 -0.500000 0.866000 0.000000 0.00000 MTRIX2 1 0.866000 0.500000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 1.000000 28.87000 APPLYING THE FOLLOWING TRANSFORMATION TO THE DIMER WILL YIELD THE TETRAMER: MTRIX1 2 -1.000000 0.000000 0.000000 76.40000 MTRIX2 2 0.000000 -1.000000 0.000000 132.20000 MTRIX3 2 0.000000 0.000000 1.000000 0.00000 A ALA 7 A ALA 6 HELX_P A HIS 16 A HIS 15 1 H1 10 A PRO 62 A PRO 61 HELX_P A ALA 72 A ALA 71 1 H2 11 A ARG 85 A ARG 84 HELX_P A ILE 97 A ILE 96 1 H3 13 A GLY 111 A GLY 110 HELX_P A THR 126 A THR 125 1 H4 16 A GLY 143 A GLY 142 HELX_P A SER 147 A SER 146 1 H5 5 A TYR 185 A TYR 184 HELX_P A GLN 199 A GLN 198 1 H6 15 A TYR 225 A TYR 224 HELX_P A ALA 235 A ALA 234 1 H7 11 A ALA 257 A ALA 256 HELX_P A ASP 261 A ASP 260 1 H8 5 A ALA 287 A ALA 286 HELX_P A LEU 296 A LEU 295 1 H9 10 A PRO 308 A PRO 307 HELX_P A ARG 323 A ARG 322 1 H10 16 A LEU 326 A LEU 325 HELX_P A ARG 347 A ARG 346 1 H11 22 A LEU 378 A LEU 377 HELX_P A LEU 389 A LEU 388 1 H12 12 A GLU 415 A GLU 414 HELX_P A ARG 431 A ARG 430 1 H13 17 covale 1.300 A LYS 272 A NZ LYS 271 1_555 A PLP 437 D C4A PLP 1_555 metalc 2.426 A NA 435 B NA NA 1_555 A ALA 95 A O ALA 94 1_555 metalc 2.421 A NA 435 B NA NA 1_555 A LEU 102 A O LEU 101 1_555 metalc 2.292 A NA 435 B NA NA 1_555 A HOH 540 F O HOH 1_555 metalc 2.230 A NA 435 B NA NA 1_555 A PRO 99 A O PRO 98 1_555 metalc 2.409 A NA 435 B NA NA 1_555 A THR 98 A O THR 97 1_555 metalc 1.915 A LI 436 C LI LI 1_555 A HOH 552 F O HOH 1_555 metalc 1.923 A LI 436 C LI LI 1_555 A LEU 78 A O LEU 77 1_555 metalc 1.900 A LI 436 C LI LI 1_555 A HOH 539 F O HOH 1_555 metalc 1.868 A LI 436 C LI LI 1_555 A ASP 307 A OD1 ASP 306 1_555 metalc 2.858 A THR 98 A OG1 THR 97 1_555 A NA 435 B NA NA 1_555 LYASE LYASE DGDA_BURCE UNP 1 1 P16932 SLNDDATFWRNARQHLVRYGGTFEPMIIERAKGSFVYDADGRAILDFTSGQMSAVLGHCHPEIVSVIGEYAGKLDHLFSG MLSRPVVDLATRLANITPPGLDRALLLSTGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTGAAASATYSAGRKGVGPAA VGSFAIPAPFTYRPRFERNGAYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPDGYMAALKRKCEARGMLLI LDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAIVTSAAIEERAHELGYLFYTTHVSDPLPAAVGLRVLDVV QRDGLVARANVMGDRLRRGLLDLMERFDCIGDVRGRGLLLGVEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGM GGVFRIAPPLTVSEDEIDLGLSLLGQAIERAL 1 432 1DGD 2 433 P16932 A 1 1 432 1 GLN CONFLICT HIS 15 1DGD A P16932 UNP 14 14 3 7 anti-parallel anti-parallel anti-parallel anti-parallel parallel parallel parallel parallel A GLU 30 A GLU 29 A LYS 33 A LYS 32 A PHE 36 A PHE 35 A ASP 39 A ASP 38 A ARG 43 A ARG 42 A ASP 47 A ASP 46 A ARG 104 A ARG 103 A SER 109 A SER 108 A LEU 280 A LEU 279 A THR 285 A THR 284 A ASP 266 A ASP 265 A LEU 270 A LEU 269 A LEU 239 A LEU 238 A GLU 244 A GLU 243 A LEU 204 A LEU 203 A ALA 209 A ALA 208 A GLU 130 A GLU 129 A PHE 134 A PHE 133 A GLY 163 A GLY 162 A ILE 167 A ILE 166 ACTIVE SITE: THE COFACTOR PLP IS COVALENTLY BOUND Author 22 METAL BINDING SITE 1 (NEAR THE ACTIVE SITE): LIGANDS TO THE LI+ ION ARE INDICATED Author 5 METAL BINDING SITE 2: LIGANDS TO THE NA+ ION ARE INDICATED Author 6 BINDING SITE FOR RESIDUE NA A 435 Software 5 BINDING SITE FOR RESIDUE PLP A 437 Software 16 BINDING SITE FOR RESIDUE MES A 434 Software 8 A GLN 52 A GLN 51 22 1_555 A MET 53 A MET 52 22 1_555 A PHE 79 A PHE 78 22 1_555 A THR 110 A THR 109 22 1_555 A GLY 111 A GLY 110 22 1_555 A ASN 115 A ASN 114 22 1_555 A SER 137 A SER 136 22 1_555 A TRP 138 A TRP 137 22 1_555 A MET 141 A MET 140 22 1_555 A GLU 210 A GLU 209 22 1_555 A SER 214 A SER 213 22 1_555 A SER 215 A SER 214 22 1_555 A ASP 243 A ASP 242 22 1_555 A ALA 245 A ALA 244 22 1_555 A GLN 246 A GLN 245 22 1_555 A LYS 272 A LYS 271 22 1_555 A PLP 437 D PLP 22 1_555 A TYR 301 A TYR 300 22 1_555 A THR 303 A THR 302 22 1_555 A ASN 394 A ASN 393 22 1_555 A ARG 406 A ARG 405 22 1_555 A MES 434 E MES 22 1_555 A LEU 78 A LEU 77 5 1_555 A ASP 307 A ASP 306 5 1_555 A HOH 539 F HOH 5 1_555 A HOH 552 F HOH 5 1_555 A LI 436 C LI 5 1_555 A ALA 95 A ALA 94 6 1_555 A THR 98 A THR 97 6 1_555 A PRO 99 A PRO 98 6 1_555 A LEU 102 A LEU 101 6 1_555 A HOH 540 F HOH 6 1_555 A NA 435 B NA 6 1_555 A ALA 95 A ALA 94 5 1_555 A THR 98 A THR 97 5 1_555 A PRO 99 A PRO 98 5 1_555 A LEU 102 A LEU 101 5 1_555 A HOH 540 F HOH 5 1_555 A THR 110 A THR 109 16 1_555 A GLY 111 A GLY 110 16 1_555 A ALA 112 A ALA 111 16 1_555 A ASN 115 A ASN 114 16 1_555 A TRP 138 A TRP 137 16 1_555 A HIS 139 A HIS 138 16 1_555 A GLU 210 A GLU 209 16 1_555 A ASP 243 A ASP 242 16 1_555 A ALA 245 A ALA 244 16 1_555 A GLN 246 A GLN 245 16 1_555 A LYS 272 A LYS 271 16 1_555 A THR 302 A THR 301 16 7_555 A THR 303 A THR 302 16 7_555 A MES 434 E MES 16 1_555 A HOH 555 F HOH 16 7_555 A HOH 557 F HOH 16 1_555 A GLN 52 A GLN 51 8 1_555 A TRP 138 A TRP 137 8 1_555 A ALA 152 A ALA 151 8 1_555 A SER 215 A SER 214 8 1_555 A GLN 246 A GLN 245 8 1_555 A LYS 272 A LYS 271 8 1_555 A ARG 406 A ARG 405 8 1_555 A PLP 437 D PLP 8 1_555 181 P 64 2 2