0.020442 0.000000 0.000000 0.000000 0.018416 0.000000 0.000000 0.000000 0.015013 0.000000 0.000000 0.000000 Steegborn, C. Schweizer, U. Schlicker, C. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 90.000 90.000 48.920 54.300 66.610 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 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 O2 Se 168.053 y SELENOCYSTEINE 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 Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 111 10526 10.1073/pnas.1323873111 25002520 Crystal structure of mammalian selenocysteine-dependent iodothyronine deiodinase suggests a peroxiredoxin-like catalytic mechanism. 2014 100 1 CCD 2008-11-13 ADSC QUANTUM 4 SINGLE WAVELENGTH M x-ray 1 0.9795 1.0 ID14-4 ESRF 0.9795 SYNCHROTRON ESRF BEAMLINE ID14-4 six N-terminal residues are cloning artifact; three C-terminal residues not visible in electron density 21696.639 Type III iodothyronine deiodinase 1.97.1.11 yes 1 man polymer 18.015 water 93 nat water 5DIII,DIOIII,Type 3 DI,Type-III 5'-deiodinase no yes GIDPFTGQKLDFFKQAHEGGPAPNSEVVRPDGFQSQRILDYAQGTRPLVLNFGSCTCPPF(MSE)AR(MSE)SAFQRLVT KYQRDVDFLIIYIEEAHPSDGWVTTDSPYVIPQHRSLEDRVSAARVLQQGAPGCALVLDT(MSE)ANSSSSAYGAYFERL YVIQSGTI(MSE)YQGGRGPDGYQVSELRTWLERYDEQLHGTRPHRF GIDPFTGQKLDFFKQAHEGGPAPNSEVVRPDGFQSQRILDYAQGTRPLVLNFGSCTCPPFMARMSAFQRLVTKYQRDVDF LIIYIEEAHPSDGWVTTDSPYVIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQG GRGPDGYQVSELRTWLERYDEQLHGTRPHRF 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 House mouse sample 1 191 Dio3 10090 Mus musculus 562 Escherichia coli plasmid Biological sequence pET151 TOPO 1 2.08 40.90 VAPOR DIFFUSION 7.0 20 % PEG 3350, 0.2 M Ammoniumcitrate 293 repository Initial release Data collection 1 0 2014-07-23 1 1 2015-02-04 N RCSB Y PDBE 2014-06-13 REL REL 1 A O HOH 482 6.85 HOH water HOH 226 2 HOH HOH 401 A HOH 18 2 HOH HOH 402 A HOH 27 2 HOH HOH 403 A HOH 45 2 HOH HOH 404 A HOH 219 2 HOH HOH 405 A HOH 15 2 HOH HOH 406 A HOH 148 2 HOH HOH 407 A HOH 228 2 HOH HOH 408 A HOH 8 2 HOH HOH 409 A HOH 16 2 HOH HOH 410 A HOH 147 2 HOH HOH 411 A HOH 215 2 HOH HOH 412 A HOH 153 2 HOH HOH 413 A HOH 32 2 HOH HOH 414 A HOH 13 2 HOH HOH 415 A HOH 19 2 HOH HOH 416 A HOH 235 2 HOH HOH 417 A HOH 106 2 HOH HOH 418 A HOH 92 2 HOH HOH 419 A HOH 172 2 HOH HOH 420 A HOH 210 2 HOH HOH 421 A HOH 93 2 HOH HOH 422 A HOH 149 2 HOH HOH 423 A HOH 90 2 HOH HOH 424 A HOH 94 2 HOH HOH 425 A HOH 14 2 HOH HOH 426 A HOH 162 2 HOH HOH 427 A HOH 155 2 HOH HOH 428 A HOH 161 2 HOH HOH 429 A HOH 7 2 HOH HOH 430 A HOH 10 2 HOH HOH 431 A HOH 6 2 HOH HOH 432 A HOH 28 2 HOH HOH 433 A HOH 193 2 HOH HOH 434 A HOH 195 2 HOH HOH 435 A HOH 179 2 HOH HOH 436 A HOH 2 2 HOH HOH 437 A HOH 31 2 HOH HOH 438 A HOH 43 2 HOH HOH 439 A HOH 185 2 HOH HOH 440 A HOH 180 2 HOH HOH 441 A HOH 29 2 HOH HOH 442 A HOH 38 2 HOH HOH 443 A HOH 194 2 HOH HOH 444 A HOH 198 2 HOH HOH 445 A HOH 134 2 HOH HOH 446 A HOH 150 2 HOH HOH 447 A HOH 214 2 HOH HOH 448 A HOH 233 2 HOH HOH 449 A HOH 1 2 HOH HOH 450 A HOH 3 2 HOH HOH 451 A HOH 5 2 HOH HOH 452 A HOH 11 2 HOH HOH 453 A HOH 12 2 HOH HOH 454 A HOH 17 2 HOH HOH 455 A HOH 22 2 HOH HOH 456 A HOH 23 2 HOH HOH 457 A HOH 24 2 HOH HOH 458 A HOH 30 2 HOH HOH 459 A HOH 33 2 HOH HOH 460 A HOH 40 2 HOH HOH 461 A HOH 41 2 HOH HOH 462 A HOH 42 2 HOH HOH 463 A HOH 47 2 HOH HOH 464 A HOH 49 2 HOH HOH 465 A HOH 50 2 HOH HOH 466 A HOH 55 2 HOH HOH 467 A HOH 58 2 HOH HOH 468 A HOH 59 2 HOH HOH 469 A HOH 88 2 HOH HOH 470 A HOH 95 2 HOH HOH 471 A HOH 97 2 HOH HOH 472 A HOH 98 2 HOH HOH 473 A HOH 103 2 HOH HOH 474 A HOH 107 2 HOH HOH 475 A HOH 133 2 HOH HOH 476 A HOH 136 2 HOH HOH 477 A HOH 154 2 HOH HOH 478 A HOH 156 2 HOH HOH 479 A HOH 160 2 HOH HOH 480 A HOH 184 2 HOH HOH 481 A HOH 191 2 HOH HOH 482 A HOH 197 2 HOH HOH 483 A HOH 201 2 HOH HOH 484 A HOH 202 2 HOH HOH 485 A HOH 216 2 HOH HOH 486 A HOH 220 2 HOH HOH 487 A HOH 221 2 HOH HOH 488 A HOH 223 2 HOH HOH 489 A HOH 227 2 HOH HOH 490 A HOH 237 2 HOH HOH 491 A HOH 247 2 HOH HOH 492 A HOH 248 2 HOH HOH 493 A GLY 114 n 1 GLY 114 A ILE 115 n 2 ILE 115 A ASP 116 n 3 ASP 116 A PRO 117 n 4 PRO 117 A PHE 118 n 5 PHE 118 A THR 119 n 6 THR 119 A GLY 120 n 7 GLY 120 A GLN 121 n 8 GLN 121 A LYS 122 n 9 LYS 122 A LEU 123 n 10 LEU 123 A ASP 124 n 11 ASP 124 A PHE 125 n 12 PHE 125 A PHE 126 n 13 PHE 126 A LYS 127 n 14 LYS 127 A GLN 128 n 15 GLN 128 A ALA 129 n 16 ALA 129 A HIS 130 n 17 HIS 130 A GLU 131 n 18 GLU 131 A GLY 132 n 19 GLY 132 A GLY 133 n 20 GLY 133 A PRO 134 n 21 PRO 134 A ALA 135 n 22 ALA 135 A PRO 136 n 23 PRO 136 A ASN 137 n 24 ASN 137 A SER 138 n 25 SER 138 A GLU 139 n 26 GLU 139 A VAL 140 n 27 VAL 140 A VAL 141 n 28 VAL 141 A ARG 142 n 29 ARG 142 A PRO 143 n 30 PRO 143 A ASP 144 n 31 ASP 144 A GLY 145 n 32 GLY 145 A PHE 146 n 33 PHE 146 A GLN 147 n 34 GLN 147 A SER 148 n 35 SER 148 A GLN 149 n 36 GLN 149 A ARG 150 n 37 ARG 150 A ILE 151 n 38 ILE 151 A LEU 152 n 39 LEU 152 A ASP 153 n 40 ASP 153 A TYR 154 n 41 TYR 154 A ALA 155 n 42 ALA 155 A GLN 156 n 43 GLN 156 A GLY 157 n 44 GLY 157 A THR 158 n 45 THR 158 A ARG 159 n 46 ARG 159 A PRO 160 n 47 PRO 160 A LEU 161 n 48 LEU 161 A VAL 162 n 49 VAL 162 A LEU 163 n 50 LEU 163 A ASN 164 n 51 ASN 164 A PHE 165 n 52 PHE 165 A GLY 166 n 53 GLY 166 A SER 167 n 54 SER 167 A CYS 168 n 55 CYS 168 A THR 169 n 56 THR 169 A CYS 170 n 57 CYS 170 A PRO 171 n 58 PRO 171 A PRO 172 n 59 PRO 172 A PHE 173 n 60 PHE 173 A MSE 174 n 61 MSE 174 A ALA 175 n 62 ALA 175 A ARG 176 n 63 ARG 176 A MSE 177 n 64 MSE 177 A SER 178 n 65 SER 178 A ALA 179 n 66 ALA 179 A PHE 180 n 67 PHE 180 A GLN 181 n 68 GLN 181 A ARG 182 n 69 ARG 182 A LEU 183 n 70 LEU 183 A VAL 184 n 71 VAL 184 A THR 185 n 72 THR 185 A LYS 186 n 73 LYS 186 A TYR 187 n 74 TYR 187 A GLN 188 n 75 GLN 188 A ARG 189 n 76 ARG 189 A ASP 190 n 77 ASP 190 A VAL 191 n 78 VAL 191 A ASP 192 n 79 ASP 192 A PHE 193 n 80 PHE 193 A LEU 194 n 81 LEU 194 A ILE 195 n 82 ILE 195 A ILE 196 n 83 ILE 196 A TYR 197 n 84 TYR 197 A ILE 198 n 85 ILE 198 A GLU 199 n 86 GLU 199 A GLU 200 n 87 GLU 200 A ALA 201 n 88 ALA 201 A HIS 202 n 89 HIS 202 A PRO 203 n 90 PRO 203 A SER 204 n 91 SER 204 A ASP 205 n 92 ASP 205 A GLY 206 n 93 GLY 206 A TRP 207 n 94 TRP 207 A VAL 208 n 95 VAL 208 A THR 209 n 96 THR 209 A THR 210 n 97 THR 210 A ASP 211 n 98 ASP 211 A SER 212 n 99 SER 212 A PRO 213 n 100 PRO 213 A TYR 214 n 101 TYR 214 A VAL 215 n 102 VAL 215 A ILE 216 n 103 ILE 216 A PRO 217 n 104 PRO 217 A GLN 218 n 105 GLN 218 A HIS 219 n 106 HIS 219 A ARG 220 n 107 ARG 220 A SER 221 n 108 SER 221 A LEU 222 n 109 LEU 222 A GLU 223 n 110 GLU 223 A ASP 224 n 111 ASP 224 A ARG 225 n 112 ARG 225 A VAL 226 n 113 VAL 226 A SER 227 n 114 SER 227 A ALA 228 n 115 ALA 228 A ALA 229 n 116 ALA 229 A ARG 230 n 117 ARG 230 A VAL 231 n 118 VAL 231 A LEU 232 n 119 LEU 232 A GLN 233 n 120 GLN 233 A GLN 234 n 121 GLN 234 A GLY 235 n 122 GLY 235 A ALA 236 n 123 ALA 236 A PRO 237 n 124 PRO 237 A GLY 238 n 125 GLY 238 A CYS 239 n 126 CYS 239 A ALA 240 n 127 ALA 240 A LEU 241 n 128 LEU 241 A VAL 242 n 129 VAL 242 A LEU 243 n 130 LEU 243 A ASP 244 n 131 ASP 244 A THR 245 n 132 THR 245 A MSE 246 n 133 MSE 246 A ALA 247 n 134 ALA 247 A ASN 248 n 135 ASN 248 A SER 249 n 136 SER 249 A SER 250 n 137 SER 250 A SER 251 n 138 SER 251 A SER 252 n 139 SER 252 A ALA 253 n 140 ALA 253 A TYR 254 n 141 TYR 254 A GLY 255 n 142 GLY 255 A ALA 256 n 143 ALA 256 A TYR 257 n 144 TYR 257 A PHE 258 n 145 PHE 258 A GLU 259 n 146 GLU 259 A ARG 260 n 147 ARG 260 A LEU 261 n 148 LEU 261 A TYR 262 n 149 TYR 262 A VAL 263 n 150 VAL 263 A ILE 264 n 151 ILE 264 A GLN 265 n 152 GLN 265 A SER 266 n 153 SER 266 A GLY 267 n 154 GLY 267 A THR 268 n 155 THR 268 A ILE 269 n 156 ILE 269 A MSE 270 n 157 MSE 270 A TYR 271 n 158 TYR 271 A GLN 272 n 159 GLN 272 A GLY 273 n 160 GLY 273 A GLY 274 n 161 GLY 274 A ARG 275 n 162 ARG 275 A GLY 276 n 163 GLY 276 A PRO 277 n 164 PRO 277 A ASP 278 n 165 ASP 278 A GLY 279 n 166 GLY 279 A TYR 280 n 167 TYR 280 A GLN 281 n 168 GLN 281 A VAL 282 n 169 VAL 282 A SER 283 n 170 SER 283 A GLU 284 n 171 GLU 284 A LEU 285 n 172 LEU 285 A ARG 286 n 173 ARG 286 A THR 287 n 174 THR 287 A TRP 288 n 175 TRP 288 A LEU 289 n 176 LEU 289 A GLU 290 n 177 GLU 290 A ARG 291 n 178 ARG 291 A TYR 292 n 179 TYR 292 A ASP 293 n 180 ASP 293 A GLU 294 n 181 GLU 294 A GLN 295 n 182 GLN 295 A LEU 296 n 183 LEU 296 A HIS 297 n 184 HIS 297 A GLY 298 n 185 GLY 298 A THR 299 n 186 THR 299 A ARG 300 n 187 ARG 300 A PRO 301 n 188 PRO 301 A n 189 302 A n 190 303 A n 191 304 A software_defined_assembly PISA 1 Monomeric 0 0 10230 A MSE 174 modified residue A MSE 61 MET A MSE 177 modified residue A MSE 64 MET A MSE 246 modified residue A MSE 133 MET A MSE 270 modified residue A MSE 157 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 O GLN 149 A O GLN 36 A N VAL 140 A N VAL 27 A N VAL 141 A N VAL 28 A O LEU 243 A O LEU 130 A O VAL 242 A O VAL 129 A N TYR 197 A N TYR 84 A O ASP 192 A O ASP 79 A N VAL 162 A N VAL 49 A N LEU 161 A N LEU 48 A O ILE 264 A O ILE 151 A N VAL 263 A N VAL 150 A O MSE 270 A O MSE 157 1 A CG PHE 126 A CG PHE 13 1 Y 1 A CD1 PHE 126 A CD1 PHE 13 1 Y 1 A CD2 PHE 126 A CD2 PHE 13 1 Y 1 A CE1 PHE 126 A CE1 PHE 13 1 Y 1 A CE2 PHE 126 A CE2 PHE 13 1 Y 1 A CZ PHE 126 A CZ PHE 13 1 Y 1 A CG LYS 127 A CG LYS 14 1 Y 1 A CD LYS 127 A CD LYS 14 1 Y 1 A CE LYS 127 A CE LYS 14 1 Y 1 A NZ LYS 127 A NZ LYS 14 1 Y 1 A CG1 VAL 208 A CG1 VAL 95 1 Y 1 A CG2 VAL 208 A CG2 VAL 95 1 Y 1 A OG1 THR 209 A OG1 THR 96 1 Y 1 A CG2 THR 209 A CG2 THR 96 1 Y 1 A OG1 THR 210 A OG1 THR 97 1 Y 1 A CG2 THR 210 A CG2 THR 97 1 Y 1 A OD1 ASP 278 A OD1 ASP 165 1 Y 1 A OD2 ASP 278 A OD2 ASP 165 1 Y 1 A CD GLU 284 A CD GLU 171 1 Y 1 A OE1 GLU 284 A OE1 GLU 171 1 Y 1 A OE2 GLU 284 A OE2 GLU 171 1 Y 1 A HIS 302 A HIS 189 1 Y 1 A ARG 303 A ARG 190 1 Y 1 A PHE 304 A PHE 191 1 Y 1 A ALA 236 34.92 60.87 1 A PHE 258 74.13 -83.02 51.080 18.0 4.620 1.2700 0.0000 0.0000 -0.5400 0.0000 -0.7300 0.9300 0.9000 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY 0.2272 0.1866 0.1885 1.9000 42.0700 706 13309 14015 5.0000 95.9500 3.0350 0.0900 RANDOM 1 THROUGHOUT 0.000 SAD 0.1710 0.1520 0.8000 0.8000 1.2000 MAXIMUM LIKELIHOOD BABINET MODEL WITH MASK 1.9000 42.0700 93 1555 22.18 0 0 1462 188 0.015 0.022 1500 1.395 1.953 2038 5.862 5.000 187 34.065 22.973 74 13.826 15.000 226 16.055 15.000 14 0.098 0.200 212 0.007 0.021 1194 0.971 1.500 935 1.797 2.000 1498 2.721 3.000 565 4.236 4.500 540 0.2680 0.1860 1.9450 46 727 773 20 72.7200 1.90 20.0 4TR3 14304 14015 0.075 1 13.9 3.7 96.0 refinement REFMAC 5.5.0042 data extraction PDB_EXTRACT 3.14 data reduction XDS phasing SHELX model building ARP model building Coot Mouse iodothyronine deiodinase 3 catalytic core (E.C.1.97.1.11) Mouse iodothyronine deiodinase 3 catalytic core, SeMet-labeled active site mutant SeCys->Cys 1 N N 2 N N A LEU 152 A LEU 39 HELX_P A ALA 155 A ALA 42 5 AA1 4 A CYS 170 A CYS 57 HELX_P A ARG 176 A ARG 63 1 AA2 7 A ARG 176 A ARG 63 HELX_P A GLN 188 A GLN 75 1 AA3 13 A SER 221 A SER 108 HELX_P A GLY 235 A GLY 122 1 AA4 15 A ASN 248 A ASN 135 HELX_P A TYR 254 A TYR 141 1 AA5 7 A GLY 279 A GLY 166 HELX_P A GLY 298 A GLY 185 1 AA6 20 covale 1.340 both A PHE 173 A C PHE 60 1_555 A MSE 174 A N MSE 61 1_555 covale 1.329 both A MSE 174 A C MSE 61 1_555 A ALA 175 A N ALA 62 1_555 covale 1.334 both A ARG 176 A C ARG 63 1_555 A MSE 177 A N MSE 64 1_555 covale 1.333 both A MSE 177 A C MSE 64 1_555 A SER 178 A N SER 65 1_555 covale 1.324 both A THR 245 A C THR 132 1_555 A MSE 246 A N MSE 133 1_555 covale 1.328 both A MSE 246 A C MSE 133 1_555 A ALA 247 A N ALA 134 1_555 covale 1.329 both A ILE 269 A C ILE 156 1_555 A MSE 270 A N MSE 157 1_555 covale 1.330 both A MSE 270 A C MSE 157 1_555 A TYR 271 A N TYR 158 1_555 OXIDOREDUCTASE deiodinase, thyronine hormones, thioredoxin fold, oxidoreductase IOD3_MOUSE UNP 1 120 Q91ZI8 GQKLDFFKQAHEGGPAPNSEVVRPDGFQSQRILDYAQGTRPLVLNFGSCTUPPFMARMSAFQRLVTKYQRDVDFLIIYIE EAHPSDGWVTTDSPYVIPQHRSLEDRVSAARVLQQGAPGCALVLDTMANSSSSAYGAYFERLYVIQSGTIMYQGGRGPDG YQVSELRTWLERYDEQLHGTRPHRF 120 304 4TR3 120 304 Q91ZI8 A 1 7 191 1 expression tag GLY 114 4TR3 A Q91ZI8 UNP 1 1 expression tag ILE 115 4TR3 A Q91ZI8 UNP 2 1 expression tag ASP 116 4TR3 A Q91ZI8 UNP 3 1 expression tag PRO 117 4TR3 A Q91ZI8 UNP 4 1 expression tag PHE 118 4TR3 A Q91ZI8 UNP 5 1 expression tag THR 119 4TR3 A Q91ZI8 UNP 6 1 SEC engineered mutation CYS 170 4TR3 A Q91ZI8 UNP 170 57 7 anti-parallel anti-parallel parallel parallel anti-parallel anti-parallel A SER 148 A SER 35 A ARG 150 A ARG 37 A GLU 139 A GLU 26 A VAL 141 A VAL 28 A LEU 241 A LEU 128 A ASP 244 A ASP 131 A ASP 192 A ASP 79 A TYR 197 A TYR 84 A LEU 161 A LEU 48 A GLY 166 A GLY 53 A ARG 260 A ARG 147 A GLN 265 A GLN 152 A THR 268 A THR 155 A GLN 272 A GLN 159 19 P 21 21 21