0.012387 0.000000 0.000000 0.000000 0.012387 0.000000 0.000000 0.000000 0.007014 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.000 90.000 90.000 80.732 80.732 142.581 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 C H2 O2 46.025 FORMIC ACID 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 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 To be published 0353 Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution 10.2210/pdb3mcp/pdb pdb_00003mcp 100 1 Flat collimating mirror, toroid focusing mirror CCD 2009-07-30 MARMOSAIC 325 mm CCD Double crystal monochromator MAD M x-ray 1 0.91162 1.0 0.97911 1.0 BL9-2 SSRL 0.91162,0.97911 SYNCHROTRON SSRL BEAMLINE BL9-2 39298.441 Glucokinase 1 man polymer 92.094 GLYCEROL 2 syn non-polymer 46.025 FORMIC ACID 1 syn non-polymer 18.015 water 13 nat water no yes G(MSE)(MSE)YTNDNRIV(MSE)TLDAGGTNFVFSAIQGGKEIADPVVLPACADCLDKCLGNLVEGFKAIQAGLPEAPV AISFAFPGPADYQAGIIGDLPNFPSFRGGVALGPFLEDIFGIPVFINNDGSLFAYGEALTGVLPEINRRLREAGSTKRYK NLLGVTLGTGFGAGVVIDGELLRGDNAAGGYVWCLRNKKYPEYIVEESVSIRAV(MSE)RVYAERSGDAGARTPKEIFEI AEGIRPGNREAAIAAFEELGE(MSE)AGDALASAITLIDGLIVIGGGLSGASKYILPVLLKE(MSE)NAQTG(MSE) (MSE)DGARFGRLQKEVYDLDEEKSFAGFARGEAVEVLVPGTNRKVGYDPCKRIGVTFSKQGANRSIA(MSE)GAYVFAL NHLSK GMMYTNDNRIVMTLDAGGTNFVFSAIQGGKEIADPVVLPACADCLDKCLGNLVEGFKAIQAGLPEAPVAISFAFPGPADY QAGIIGDLPNFPSFRGGVALGPFLEDIFGIPVFINNDGSLFAYGEALTGVLPEINRRLREAGSTKRYKNLLGVTLGTGFG AGVVIDGELLRGDNAAGGYVWCLRNKKYPEYIVEESVSIRAVMRVYAERSGDAGARTPKEIFEIAEGIRPGNREAAIAAF EELGEMAGDALASAITLIDGLIVIGGGLSGASKYILPVLLKEMNAQTGMMDGARFGRLQKEVYDLDEEKSFAGFARGEAV EVLVPGTNRKVGYDPCKRIGVTFSKQGANRSIAMGAYVFALNHLSK A 400675 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 ATCC 8503 / DSM 20701 / NCTC 11152 sample BDI_1628 435591 Parabacteroides distasonis 562 Escherichia Coli HK100 Plasmid SpeedET 1 2.96 58.39 VAPOR DIFFUSION, SITTING DROP 7.3 10.0000% Glycerol, 3.6000M NaFormate, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software software struct_conn database_2 struct_ref_seq_dif struct_site repository Initial release Version format compliance Refinement description Data collection Derived calculations Refinement description Database references Derived calculations 1 0 2010-05-12 1 1 2011-07-13 1 2 2017-11-08 1 3 2019-07-17 1 4 2023-02-01 _software.classification _software.name _software.classification _software.contact_author _software.contact_author_email _software.language _software.location _software.name _software.type _software.version _struct_conn.pdbx_leaving_atom_flag _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y RCSB Y RCSB 2010-03-29 REL REL GOL GLYCEROL FMT FORMIC ACID HOH water THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLYCINE AT POSITION 61 INSTEAD OF AN ASPARTATE AND A GLUTAMATE AT POSITION 306 INSTEAD OF AN ASPARTATE. THE GLYCINE AT POSITION 61 AND GLUTAMATE AT POSITION 306 ARE SUPPORTED BY THE ELECTRON DENSITY. GOL 1 2 GOL GOL 366 A GOL 2 2 GOL GOL 367 A FMT 3 3 FMT FMT 368 A HOH 4 4 HOH HOH 369 A HOH 5 4 HOH HOH 370 A HOH 6 4 HOH HOH 371 A HOH 7 4 HOH HOH 372 A HOH 8 4 HOH HOH 373 A HOH 9 4 HOH HOH 374 A HOH 10 4 HOH HOH 375 A HOH 11 4 HOH HOH 376 A HOH 12 4 HOH HOH 377 A HOH 13 4 HOH HOH 378 A HOH 14 4 HOH HOH 379 A HOH 15 4 HOH HOH 380 A HOH 16 4 HOH HOH 381 A n 1 0 A MSE 1 n 2 MSE 1 A MSE 2 n 3 MSE 2 A TYR 3 n 4 TYR 3 A THR 4 n 5 THR 4 A ASN 5 n 6 ASN 5 A ASP 6 n 7 ASP 6 A ASN 7 n 8 ASN 7 A ARG 8 n 9 ARG 8 A ILE 9 n 10 ILE 9 A VAL 10 n 11 VAL 10 A MSE 11 n 12 MSE 11 A THR 12 n 13 THR 12 A LEU 13 n 14 LEU 13 A ASP 14 n 15 ASP 14 A ALA 15 n 16 ALA 15 A GLY 16 n 17 GLY 16 A GLY 17 n 18 GLY 17 A THR 18 n 19 THR 18 A ASN 19 n 20 ASN 19 A PHE 20 n 21 PHE 20 A VAL 21 n 22 VAL 21 A PHE 22 n 23 PHE 22 A SER 23 n 24 SER 23 A ALA 24 n 25 ALA 24 A ILE 25 n 26 ILE 25 A GLN 26 n 27 GLN 26 A GLY 27 n 28 GLY 27 A GLY 28 n 29 GLY 28 A LYS 29 n 30 LYS 29 A GLU 30 n 31 GLU 30 A ILE 31 n 32 ILE 31 A ALA 32 n 33 ALA 32 A ASP 33 n 34 ASP 33 A PRO 34 n 35 PRO 34 A VAL 35 n 36 VAL 35 A VAL 36 n 37 VAL 36 A LEU 37 n 38 LEU 37 A PRO 38 n 39 PRO 38 A ALA 39 n 40 ALA 39 A CYS 40 n 41 CYS 40 A ALA 41 n 42 ALA 41 A ASP 42 n 43 ASP 42 A CYS 43 n 44 CYS 43 A LEU 44 n 45 LEU 44 A ASP 45 n 46 ASP 45 A LYS 46 n 47 LYS 46 A CYS 47 n 48 CYS 47 A LEU 48 n 49 LEU 48 A GLY 49 n 50 GLY 49 A ASN 50 n 51 ASN 50 A LEU 51 n 52 LEU 51 A VAL 52 n 53 VAL 52 A GLU 53 n 54 GLU 53 A GLY 54 n 55 GLY 54 A PHE 55 n 56 PHE 55 A LYS 56 n 57 LYS 56 A ALA 57 n 58 ALA 57 A ILE 58 n 59 ILE 58 A GLN 59 n 60 GLN 59 A ALA 60 n 61 ALA 60 A GLY 61 n 62 GLY 61 A LEU 62 n 63 LEU 62 A PRO 63 n 64 PRO 63 A GLU 64 n 65 GLU 64 A ALA 65 n 66 ALA 65 A PRO 66 n 67 PRO 66 A VAL 67 n 68 VAL 67 A ALA 68 n 69 ALA 68 A ILE 69 n 70 ILE 69 A SER 70 n 71 SER 70 A PHE 71 n 72 PHE 71 A ALA 72 n 73 ALA 72 A PHE 73 n 74 PHE 73 A PRO 74 n 75 PRO 74 A GLY 75 n 76 GLY 75 A PRO 76 n 77 PRO 76 A ALA 77 n 78 ALA 77 A ASP 78 n 79 ASP 78 A TYR 79 n 80 TYR 79 A GLN 80 n 81 GLN 80 A ALA 81 n 82 ALA 81 A GLY 82 n 83 GLY 82 A ILE 83 n 84 ILE 83 A ILE 84 n 85 ILE 84 A GLY 85 n 86 GLY 85 A ASP 86 n 87 ASP 86 A LEU 87 n 88 LEU 87 A PRO 88 n 89 PRO 88 A ASN 89 n 90 ASN 89 A PHE 90 n 91 PHE 90 A PRO 91 n 92 PRO 91 A SER 92 n 93 SER 92 A PHE 93 n 94 PHE 93 A ARG 94 n 95 ARG 94 A GLY 95 n 96 GLY 95 A GLY 96 n 97 GLY 96 A VAL 97 n 98 VAL 97 A ALA 98 n 99 ALA 98 A LEU 99 n 100 LEU 99 A GLY 100 n 101 GLY 100 A PRO 101 n 102 PRO 101 A PHE 102 n 103 PHE 102 A LEU 103 n 104 LEU 103 A GLU 104 n 105 GLU 104 A ASP 105 n 106 ASP 105 A ILE 106 n 107 ILE 106 A PHE 107 n 108 PHE 107 A GLY 108 n 109 GLY 108 A ILE 109 n 110 ILE 109 A PRO 110 n 111 PRO 110 A VAL 111 n 112 VAL 111 A PHE 112 n 113 PHE 112 A ILE 113 n 114 ILE 113 A ASN 114 n 115 ASN 114 A ASN 115 n 116 ASN 115 A ASP 116 n 117 ASP 116 A GLY 117 n 118 GLY 117 A SER 118 n 119 SER 118 A LEU 119 n 120 LEU 119 A PHE 120 n 121 PHE 120 A ALA 121 n 122 ALA 121 A TYR 122 n 123 TYR 122 A GLY 123 n 124 GLY 123 A GLU 124 n 125 GLU 124 A ALA 125 n 126 ALA 125 A LEU 126 n 127 LEU 126 A THR 127 n 128 THR 127 A GLY 128 n 129 GLY 128 A VAL 129 n 130 VAL 129 A LEU 130 n 131 LEU 130 A PRO 131 n 132 PRO 131 A GLU 132 n 133 GLU 132 A ILE 133 n 134 ILE 133 A ASN 134 n 135 ASN 134 A ARG 135 n 136 ARG 135 A ARG 136 n 137 ARG 136 A LEU 137 n 138 LEU 137 A ARG 138 n 139 ARG 138 A GLU 139 n 140 GLU 139 A ALA 140 n 141 ALA 140 A GLY 141 n 142 GLY 141 A SER 142 n 143 SER 142 A THR 143 n 144 THR 143 A LYS 144 n 145 LYS 144 A ARG 145 n 146 ARG 145 A TYR 146 n 147 TYR 146 A LYS 147 n 148 LYS 147 A ASN 148 n 149 ASN 148 A LEU 149 n 150 LEU 149 A LEU 150 n 151 LEU 150 A GLY 151 n 152 GLY 151 A VAL 152 n 153 VAL 152 A THR 153 n 154 THR 153 A LEU 154 n 155 LEU 154 A GLY 155 n 156 GLY 155 A THR 156 n 157 THR 156 A GLY 157 n 158 GLY 157 A PHE 158 n 159 PHE 158 A GLY 159 n 160 GLY 159 A ALA 160 n 161 ALA 160 A GLY 161 n 162 GLY 161 A VAL 162 n 163 VAL 162 A VAL 163 n 164 VAL 163 A ILE 164 n 165 ILE 164 A ASP 165 n 166 ASP 165 A GLY 166 n 167 GLY 166 A GLU 167 n 168 GLU 167 A LEU 168 n 169 LEU 168 A LEU 169 n 170 LEU 169 A ARG 170 n 171 ARG 170 A GLY 171 n 172 GLY 171 A ASP 172 n 173 ASP 172 A ASN 173 n 174 ASN 173 A ALA 174 n 175 ALA 174 A ALA 175 n 176 ALA 175 A GLY 176 n 177 GLY 176 A GLY 177 n 178 GLY 177 A TYR 178 n 179 TYR 178 A VAL 179 n 180 VAL 179 A TRP 180 n 181 TRP 180 A CYS 181 n 182 CYS 181 A LEU 182 n 183 LEU 182 A ARG 183 n 184 ARG 183 A ASN 184 n 185 ASN 184 A LYS 185 n 186 LYS 185 A LYS 186 n 187 LYS 186 A TYR 187 n 188 TYR 187 A PRO 188 n 189 PRO 188 A GLU 189 n 190 GLU 189 A TYR 190 n 191 TYR 190 A ILE 191 n 192 ILE 191 A VAL 192 n 193 VAL 192 A GLU 193 n 194 GLU 193 A GLU 194 n 195 GLU 194 A SER 195 n 196 SER 195 A VAL 196 n 197 VAL 196 A SER 197 n 198 SER 197 A ILE 198 n 199 ILE 198 A ARG 199 n 200 ARG 199 A ALA 200 n 201 ALA 200 A VAL 201 n 202 VAL 201 A MSE 202 n 203 MSE 202 A ARG 203 n 204 ARG 203 A VAL 204 n 205 VAL 204 A TYR 205 n 206 TYR 205 A ALA 206 n 207 ALA 206 A GLU 207 n 208 GLU 207 A ARG 208 n 209 ARG 208 A SER 209 n 210 SER 209 A GLY 210 n 211 GLY 210 A ASP 211 n 212 ASP 211 A ALA 212 n 213 ALA 212 A GLY 213 n 214 GLY 213 A ALA 214 n 215 ALA 214 A ARG 215 n 216 ARG 215 A THR 216 n 217 THR 216 A PRO 217 n 218 PRO 217 A LYS 218 n 219 LYS 218 A GLU 219 n 220 GLU 219 A ILE 220 n 221 ILE 220 A PHE 221 n 222 PHE 221 A GLU 222 n 223 GLU 222 A ILE 223 n 224 ILE 223 A ALA 224 n 225 ALA 224 A GLU 225 n 226 GLU 225 A GLY 226 n 227 GLY 226 A ILE 227 n 228 ILE 227 A ARG 228 n 229 ARG 228 A PRO 229 n 230 PRO 229 A GLY 230 n 231 GLY 230 A ASN 231 n 232 ASN 231 A ARG 232 n 233 ARG 232 A GLU 233 n 234 GLU 233 A ALA 234 n 235 ALA 234 A ALA 235 n 236 ALA 235 A ILE 236 n 237 ILE 236 A ALA 237 n 238 ALA 237 A ALA 238 n 239 ALA 238 A PHE 239 n 240 PHE 239 A GLU 240 n 241 GLU 240 A GLU 241 n 242 GLU 241 A LEU 242 n 243 LEU 242 A GLY 243 n 244 GLY 243 A GLU 244 n 245 GLU 244 A MSE 245 n 246 MSE 245 A ALA 246 n 247 ALA 246 A GLY 247 n 248 GLY 247 A ASP 248 n 249 ASP 248 A ALA 249 n 250 ALA 249 A LEU 250 n 251 LEU 250 A ALA 251 n 252 ALA 251 A SER 252 n 253 SER 252 A ALA 253 n 254 ALA 253 A ILE 254 n 255 ILE 254 A THR 255 n 256 THR 255 A LEU 256 n 257 LEU 256 A ILE 257 n 258 ILE 257 A ASP 258 n 259 ASP 258 A GLY 259 n 260 GLY 259 A LEU 260 n 261 LEU 260 A ILE 261 n 262 ILE 261 A VAL 262 n 263 VAL 262 A ILE 263 n 264 ILE 263 A GLY 264 n 265 GLY 264 A GLY 265 n 266 GLY 265 A GLY 266 n 267 GLY 266 A LEU 267 n 268 LEU 267 A SER 268 n 269 SER 268 A GLY 269 n 270 GLY 269 A ALA 270 n 271 ALA 270 A SER 271 n 272 SER 271 A LYS 272 n 273 LYS 272 A TYR 273 n 274 TYR 273 A ILE 274 n 275 ILE 274 A LEU 275 n 276 LEU 275 A PRO 276 n 277 PRO 276 A VAL 277 n 278 VAL 277 A LEU 278 n 279 LEU 278 A LEU 279 n 280 LEU 279 A LYS 280 n 281 LYS 280 A GLU 281 n 282 GLU 281 A MSE 282 n 283 MSE 282 A ASN 283 n 284 ASN 283 A ALA 284 n 285 ALA 284 A GLN 285 n 286 GLN 285 A THR 286 n 287 THR 286 A GLY 287 n 288 GLY 287 A MSE 288 n 289 MSE 288 A MSE 289 n 290 MSE 289 A n 291 290 A n 292 291 A n 293 292 A n 294 293 A n 295 294 A n 296 295 A n 297 296 A n 298 297 A GLN 298 n 299 GLN 298 A LYS 299 n 300 LYS 299 A GLU 300 n 301 GLU 300 A VAL 301 n 302 VAL 301 A TYR 302 n 303 TYR 302 A ASP 303 n 304 ASP 303 A LEU 304 n 305 LEU 304 A ASP 305 n 306 ASP 305 A GLU 306 n 307 GLU 306 A GLU 307 n 308 GLU 307 A LYS 308 n 309 LYS 308 A SER 309 n 310 SER 309 A PHE 310 n 311 PHE 310 A ALA 311 n 312 ALA 311 A GLY 312 n 313 GLY 312 A PHE 313 n 314 PHE 313 A ALA 314 n 315 ALA 314 A ARG 315 n 316 ARG 315 A GLY 316 n 317 GLY 316 A GLU 317 n 318 GLU 317 A ALA 318 n 319 ALA 318 A VAL 319 n 320 VAL 319 A GLU 320 n 321 GLU 320 A VAL 321 n 322 VAL 321 A LEU 322 n 323 LEU 322 A VAL 323 n 324 VAL 323 A PRO 324 n 325 PRO 324 A GLY 325 n 326 GLY 325 A THR 326 n 327 THR 326 A ASN 327 n 328 ASN 327 A ARG 328 n 329 ARG 328 A LYS 329 n 330 LYS 329 A VAL 330 n 331 VAL 330 A GLY 331 n 332 GLY 331 A TYR 332 n 333 TYR 332 A ASP 333 n 334 ASP 333 A PRO 334 n 335 PRO 334 A CYS 335 n 336 CYS 335 A LYS 336 n 337 LYS 336 A ARG 337 n 338 ARG 337 A ILE 338 n 339 ILE 338 A GLY 339 n 340 GLY 339 A VAL 340 n 341 VAL 340 A THR 341 n 342 THR 341 A PHE 342 n 343 PHE 342 A SER 343 n 344 SER 343 A LYS 344 n 345 LYS 344 A GLN 345 n 346 GLN 345 A GLY 346 n 347 GLY 346 A ALA 347 n 348 ALA 347 A ASN 348 n 349 ASN 348 A ARG 349 n 350 ARG 349 A SER 350 n 351 SER 350 A ILE 351 n 352 ILE 351 A ALA 352 n 353 ALA 352 A MSE 353 n 354 MSE 353 A GLY 354 n 355 GLY 354 A ALA 355 n 356 ALA 355 A TYR 356 n 357 TYR 356 A VAL 357 n 358 VAL 357 A PHE 358 n 359 PHE 358 A ALA 359 n 360 ALA 359 A LEU 360 n 361 LEU 360 A ASN 361 n 362 ASN 361 A HIS 362 n 363 HIS 362 A LEU 363 n 364 LEU 363 A n 365 364 A n 366 365 A author_and_software_defined_assembly PISA 2 dimeric 6220 -39 28200 A MSE 1 SELENOMETHIONINE A MSE 2 MET A MSE 2 SELENOMETHIONINE A MSE 3 MET A MSE 11 SELENOMETHIONINE A MSE 12 MET A MSE 202 SELENOMETHIONINE A MSE 203 MET A MSE 245 SELENOMETHIONINE A MSE 246 MET A MSE 282 SELENOMETHIONINE A MSE 283 MET A MSE 288 SELENOMETHIONINE A MSE 289 MET A MSE 289 SELENOMETHIONINE A MSE 290 MET A MSE 353 SELENOMETHIONINE A MSE 354 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 142.5810000000 A O LYS 29 A O LYS 30 A N GLN 26 A N GLN 27 A N PHE 22 A N PHE 23 A O VAL 35 A O VAL 36 A O LYS 29 A O LYS 30 A N GLN 26 A N GLN 27 A O ILE 25 A O ILE 26 A N VAL 10 A N VAL 11 A N MSE 11 A N MSE 12 A O ALA 68 A O ALA 69 A N ILE 69 A N ILE 70 A O PHE 112 A O PHE 113 A N ASP 78 A N ASP 79 A O ILE 83 A O ILE 84 A O GLU 167 A O GLU 168 A N ILE 164 A N ILE 165 A O GLY 161 A O GLY 162 A N GLY 151 A N GLY 152 A N LEU 154 A N LEU 155 A O GLY 264 A O GLY 265 A N ILE 261 A N ILE 262 A O GLY 339 A O GLY 340 A O ILE 338 A O ILE 339 A N GLU 300 A N GLU 301 A N VAL 321 A N VAL 322 A O VAL 330 A O VAL 331 1 A CG ASN 5 A CG ASN 6 1 Y 1 A OD1 ASN 5 A OD1 ASN 6 1 Y 1 A ND2 ASN 5 A ND2 ASN 6 1 Y 1 A CG ASN 7 A CG ASN 8 1 Y 1 A OD1 ASN 7 A OD1 ASN 8 1 Y 1 A ND2 ASN 7 A ND2 ASN 8 1 Y 1 A CG LYS 29 A CG LYS 30 1 Y 1 A CD LYS 29 A CD LYS 30 1 Y 1 A CE LYS 29 A CE LYS 30 1 Y 1 A NZ LYS 29 A NZ LYS 30 1 Y 1 A CD GLU 30 A CD GLU 31 1 Y 1 A OE1 GLU 30 A OE1 GLU 31 1 Y 1 A OE2 GLU 30 A OE2 GLU 31 1 Y 1 A CG LEU 44 A CG LEU 45 1 Y 1 A CD1 LEU 44 A CD1 LEU 45 1 Y 1 A CD2 LEU 44 A CD2 LEU 45 1 Y 1 A CG LYS 46 A CG LYS 47 1 Y 1 A CD LYS 46 A CD LYS 47 1 Y 1 A CE LYS 46 A CE LYS 47 1 Y 1 A NZ LYS 46 A NZ LYS 47 1 Y 1 A CD GLU 64 A CD GLU 65 1 Y 1 A OE1 GLU 64 A OE1 GLU 65 1 Y 1 A OE2 GLU 64 A OE2 GLU 65 1 Y 1 A OG SER 92 A OG SER 93 1 Y 1 A NH1 ARG 94 A NH1 ARG 95 1 Y 1 A NH2 ARG 94 A NH2 ARG 95 1 Y 1 A CG ARG 145 A CG ARG 146 1 Y 1 A CD ARG 145 A CD ARG 146 1 Y 1 A NE ARG 145 A NE ARG 146 1 Y 1 A CZ ARG 145 A CZ ARG 146 1 Y 1 A NH1 ARG 145 A NH1 ARG 146 1 Y 1 A NH2 ARG 145 A NH2 ARG 146 1 Y 1 A NE ARG 183 A NE ARG 184 1 Y 1 A CZ ARG 183 A CZ ARG 184 1 Y 1 A NH1 ARG 183 A NH1 ARG 184 1 Y 1 A NH2 ARG 183 A NH2 ARG 184 1 Y 1 A CG GLU 189 A CG GLU 190 1 Y 1 A CD GLU 189 A CD GLU 190 1 Y 1 A OE1 GLU 189 A OE1 GLU 190 1 Y 1 A OE2 GLU 189 A OE2 GLU 190 1 Y 1 A CZ ARG 215 A CZ ARG 216 1 Y 1 A NH1 ARG 215 A NH1 ARG 216 1 Y 1 A NH2 ARG 215 A NH2 ARG 216 1 Y 1 A CD LYS 218 A CD LYS 219 1 Y 1 A CE LYS 218 A CE LYS 219 1 Y 1 A NZ LYS 218 A NZ LYS 219 1 Y 1 A NZ LYS 280 A NZ LYS 281 1 Y 1 A OE1 GLU 306 A OE1 GLU 307 1 Y 1 A OE2 GLU 306 A OE2 GLU 307 1 Y 1 A NZ LYS 308 A NZ LYS 309 1 Y 1 A OG1 THR 326 A OG1 THR 327 1 Y 1 A CG2 THR 326 A CG2 THR 327 1 Y 1 A CZ ARG 328 A CZ ARG 329 1 Y 1 A NH1 ARG 328 A NH1 ARG 329 1 Y 1 A NH2 ARG 328 A NH2 ARG 329 1 Y 1 A CD LYS 329 A CD LYS 330 1 Y 1 A CE LYS 329 A CE LYS 330 1 Y 1 A NZ LYS 329 A NZ LYS 330 1 Y 1 A CG1 VAL 330 A CG1 VAL 331 1 Y 1 A CG2 VAL 330 A CG2 VAL 331 1 Y 1 A GLY 0 A GLY 1 1 Y 1 A ASP 290 A ASP 291 1 Y 1 A GLY 291 A GLY 292 1 Y 1 A ALA 292 A ALA 293 1 Y 1 A ARG 293 A ARG 294 1 Y 1 A PHE 294 A PHE 295 1 Y 1 A GLY 295 A GLY 296 1 Y 1 A ARG 296 A ARG 297 1 Y 1 A LEU 297 A LEU 298 1 Y 1 A SER 364 A SER 365 1 Y 1 A LYS 365 A LYS 366 1 Y 1 A THR 18 83.92 -43.90 1 A PRO 63 -64.15 -73.33 1 A ALA 68 178.80 -178.07 1 A ASP 165 37.91 57.95 1 A TYR 187 -147.50 59.47 1 A PRO 188 -38.22 -31.35 1 A SER 197 179.20 173.35 1 A ASP 258 60.26 61.09 1 A PRO 324 -39.13 124.39 94.43 53.803 22.42 -1.800 0.000 0.000 -1.800 0.000 3.600 0.931 0.907 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) AND FORMIC ACID FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. 0.249 0.206 0.209 3.000 28.748 477 9970 4.800 99.810 1.00 0.75 18.642 0.336 RANDOM 1 THROUGHOUT 0.00 MAD 0.400 0.800 0.800 1.400 MAXIMUM LIKELIHOOD WITH PHASES MASK 3.000 28.748 13 2618 15 0 2590 0.010 0.022 2650 0.001 0.020 1770 0.919 1.980 3584 0.682 3.000 4318 3.396 5.000 353 27.812 24.369 103 13.335 15.000 406 11.117 15.000 14 0.060 0.200 400 0.006 0.021 3023 0.001 0.020 533 0.839 2.000 1746 0.064 2.000 739 1.722 4.000 2757 2.578 6.000 904 4.437 8.000 827 0.343 0.297 3.078 30 680 710 20 99.720 70.492 3.00 28.748 3MCP 10015 0.130 0.130 1 14.800 7.000 99.900 0.716 3.00 3.08 1.1 5232 714 0.716 7.30 100.00 0.605 3.08 3.16 1.3 5022 697 0.605 7.20 100.00 0.478 3.16 3.25 1.6 4968 691 0.478 7.20 100.00 0.375 3.25 3.35 2.0 4790 663 0.375 7.20 100.00 0.322 3.35 3.46 2.3 4587 641 0.322 7.20 100.00 0.239 3.46 3.59 3.2 4500 628 0.239 7.20 100.00 0.190 3.59 3.72 3.9 4360 607 0.190 7.20 100.00 0.164 3.72 3.87 4.6 4139 581 0.164 7.10 100.00 0.141 3.87 4.05 5.2 4023 567 0.141 7.10 100.00 0.115 4.05 4.24 6.5 3890 546 0.115 7.10 100.00 0.100 4.24 4.47 6.9 3576 510 0.100 7.00 100.00 0.090 4.47 4.74 7.9 3475 495 0.090 7.00 100.00 0.080 4.74 5.07 9.1 3177 458 0.080 6.90 100.00 0.087 5.07 5.48 8.3 3066 442 0.087 6.90 100.00 0.091 5.48 6.00 8.0 2770 404 0.091 6.90 100.00 0.083 6.00 6.71 8.7 2586 380 0.083 6.80 100.00 0.058 6.71 7.75 11.7 2158 326 0.058 6.60 100.00 0.047 7.75 9.49 13.6 1886 293 0.047 6.40 100.00 0.040 9.49 13.42 15.2 1445 238 0.040 6.10 100.00 0.046 13.42 28.75 13.0 703 134 0.046 5.20 90.60 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0102 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data scaling Phil R. Evans pre@mrc-lmb.cam.ac.uk 5/04/2004 Fortran_77 http://www.ccp4.ac.uk/dist/html/scala.html SCALA other 3.2.5 data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.006 data reduction MOSFLM phasing SHELXD phasing autoSHARP Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution 1 N N 2 N N 2 N N 3 N N 4 N N A CYS 43 A CYS 44 HELX_P A ALA 60 A ALA 61 1 1 18 A PHE 90 A PHE 91 HELX_P A ARG 94 A ARG 95 5 2 5 A ALA 98 A ALA 99 HELX_P A GLY 108 A GLY 109 1 3 11 A ASN 115 A ASN 116 HELX_P A THR 127 A THR 128 1 4 13 A GLY 128 A GLY 129 HELX_P A ALA 140 A ALA 141 1 5 13 A ILE 191 A ILE 192 HELX_P A SER 195 A SER 196 5 6 5 A SER 197 A SER 198 HELX_P A SER 209 A SER 210 1 7 13 A THR 216 A THR 217 HELX_P A GLU 225 A GLU 226 1 8 10 A ASN 231 A ASN 232 HELX_P A ASP 258 A ASP 259 1 9 28 A GLY 265 A GLY 266 HELX_P A GLY 269 A GLY 270 5 10 5 A ALA 270 A ALA 271 HELX_P A THR 286 A THR 287 1 11 17 A GLU 306 A GLU 307 HELX_P A GLY 316 A GLY 317 1 12 11 A GLY 346 A GLY 347 HELX_P A LEU 363 A LEU 364 1 13 18 covale 1.331 both A MSE 1 A C MSE 2 1_555 A MSE 2 A N MSE 3 1_555 covale 1.342 both A MSE 2 A C MSE 3 1_555 A TYR 3 A N TYR 4 1_555 covale 1.329 both A VAL 10 A C VAL 11 1_555 A MSE 11 A N MSE 12 1_555 covale 1.321 both A MSE 11 A C MSE 12 1_555 A THR 12 A N THR 13 1_555 covale 1.328 both A VAL 201 A C VAL 202 1_555 A MSE 202 A N MSE 203 1_555 covale 1.328 both A MSE 202 A C MSE 203 1_555 A ARG 203 A N ARG 204 1_555 covale 1.336 both A GLU 244 A C GLU 245 1_555 A MSE 245 A N MSE 246 1_555 covale 1.328 both A MSE 245 A C MSE 246 1_555 A ALA 246 A N ALA 247 1_555 covale 1.324 both A GLU 281 A C GLU 282 1_555 A MSE 282 A N MSE 283 1_555 covale 1.337 both A MSE 282 A C MSE 283 1_555 A ASN 283 A N ASN 284 1_555 covale 1.337 both A GLY 287 A C GLY 288 1_555 A MSE 288 A N MSE 289 1_555 covale 1.342 both A MSE 288 A C MSE 289 1_555 A MSE 289 A N MSE 290 1_555 covale 1.333 both A ALA 352 A C ALA 353 1_555 A MSE 353 A N MSE 354 1_555 covale 1.323 both A MSE 353 A C MSE 354 1_555 A GLY 354 A N GLY 355 1_555 TRANSFERASE Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, TRANSFERASE A GLY 75 A GLY 76 1 A PRO 76 A PRO 77 6.06 A6LCG6_PARD8 UNP 1 1 A6LCG6 MMYTNDNRIVMTLDAGGTNFVFSAIQGGKEIADPVVLPACADCLDKCLGNLVEGFKAIQADLPEAPVAISFAFPGPADYQ AGIIGDLPNFPSFRGGVALGPFLEDIFGIPVFINNDGSLFAYGEALTGVLPEINRRLREAGSTKRYKNLLGVTLGTGFGA GVVIDGELLRGDNAAGGYVWCLRNKKYPEYIVEESVSIRAVMRVYAERSGDAGARTPKEIFEIAEGIRPGNREAAIAAFE ELGEMAGDALASAITLIDGLIVIGGGLSGASKYILPVLLKEMNAQTGMMDGARFGRLQKEVYDLDDEKSFAGFARGEAVE VLVPGTNRKVGYDPCKRIGVTFSKQGANRSIAMGAYVFALNHLSK 1 365 3MCP 1 365 A6LCG6 A 1 2 366 1 expression tag GLY 0 3MCP A A6LCG6 UNP 1 1 ASP see remark 999 GLY 61 3MCP A A6LCG6 UNP 61 62 1 ASP see remark 999 GLU 306 3MCP A A6LCG6 UNP 306 307 3 5 2 6 2 anti-parallel anti-parallel anti-parallel anti-parallel parallel parallel anti-parallel anti-parallel anti-parallel parallel parallel parallel anti-parallel A LYS 29 A LYS 30 A GLU 30 A GLU 31 A ASN 19 A ASN 20 A GLN 26 A GLN 27 A VAL 35 A VAL 36 A PRO 38 A PRO 39 A LYS 29 A LYS 30 A GLU 30 A GLU 31 A ASN 19 A ASN 20 A GLN 26 A GLN 27 A ILE 9 A ILE 10 A ASP 14 A ASP 15 A ALA 68 A ALA 69 A ALA 72 A ALA 73 A VAL 111 A VAL 112 A ASN 114 A ASN 115 A ALA 77 A ALA 78 A ASP 78 A ASP 79 A ILE 83 A ILE 84 A ILE 84 A ILE 85 A GLU 167 A GLU 168 A LEU 168 A LEU 169 A PHE 158 A PHE 159 A ILE 164 A ILE 165 A ASN 148 A ASN 149 A LEU 154 A LEU 155 A LEU 260 A LEU 261 A GLY 264 A GLY 265 A ARG 337 A ARG 338 A PHE 342 A PHE 343 A GLU 300 A GLU 301 A ASP 303 A ASP 304 A VAL 319 A VAL 320 A LEU 322 A LEU 323 A LYS 329 A LYS 330 A TYR 332 A TYR 333 BINDING SITE FOR RESIDUE GOL A 366 A GOL 366 Software 1 BINDING SITE FOR RESIDUE GOL A 367 A GOL 367 Software 4 BINDING SITE FOR RESIDUE FMT A 368 A FMT 368 Software 7 A GLY 266 A GLY 267 1 1_555 A GLY 117 A GLY 118 4 1_555 A GLY 159 A GLY 160 4 1_555 A ALA 160 A ALA 161 4 1_555 A TYR 178 A TYR 179 4 1_555 A GLU 132 A GLU 133 7 1_555 A ILE 133 A ILE 134 7 1_555 A ARG 136 A ARG 137 7 1_555 A LEU 304 A LEU 305 7 1_555 A ASP 305 A ASP 306 7 1_555 A THR 341 A THR 342 7 1_555 A LYS 344 A LYS 345 7 1_555 96 P 43 21 2