PDB Short entry for 5DGT HEADER LYASE 28-AUG-15 5DGT TITLE BENZOYLFORMATE DECARBOXYLASE H70A MUTANT AT PH 8.5 FROM PSEUDOMONAS TITLE 2 PUTIDA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENZOYLFORMATE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BFDC; COMPND 5 EC: 4.1.1.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PUTIDA; SOURCE 3 ORGANISM_TAXID: 303; SOURCE 4 GENE: MDLC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PREP7 KEYWDS BENZOYLFORMATE DECARBOXYLASE THIAMIN THIAZOLONE DIPHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,M.S.HASSON REVDAT 2 27-SEP-23 5DGT 1 REMARK LINK REVDAT 1 23-SEP-15 5DGT 0 JRNL AUTH A.K.BERA,M.S.HASSON JRNL TITL BENZOYLFORMATE DECARBOXYLASE H70A MUTANT AT PH 8.5 FROM JRNL TITL 2 PSEUDOMONAS PUTIDA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.K.BERA,L.S.POLOVNIKOVA,J.ROESTAMADJI,T.S.WIDLANSKI, REMARK 1 AUTH 2 G.L.KENYON,M.J.MCLEISH,M.S.HASSON REMARK 1 TITL MECHANISM-BASED INACTIVATION OF BENZOYLFORMATE REMARK 1 TITL 2 DECARBOXYLASE, A THIAMIN DIPHOSPHATE-DEPENDENT ENZYME. REMARK 1 REF J.AM.CHEM.SOC. V. 129 4120 2007 REMARK 1 REFN ISSN 0002-7863 REMARK 1 PMID 17367138 REMARK 1 DOI 10.1021/JA068636Z REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 213350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.144 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 10706 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.5082 - 3.3528 0.57 4262 222 0.2118 0.1986 REMARK 3 2 3.3528 - 2.6634 0.83 6026 298 0.1517 0.1515 REMARK 3 3 2.6634 - 2.3273 0.88 6344 353 0.1320 0.1449 REMARK 3 4 2.3273 - 2.1148 0.91 6583 339 0.1247 0.1245 REMARK 3 5 2.1148 - 1.9634 0.95 6852 339 0.1234 0.1270 REMARK 3 6 1.9634 - 1.8477 0.97 6918 378 0.1230 0.1413 REMARK 3 7 1.8477 - 1.7552 0.98 7017 371 0.1204 0.1297 REMARK 3 8 1.7552 - 1.6789 0.99 7064 414 0.1212 0.1379 REMARK 3 9 1.6789 - 1.6143 0.99 7041 399 0.1222 0.1263 REMARK 3 10 1.6143 - 1.5586 0.99 7022 384 0.1196 0.1406 REMARK 3 11 1.5586 - 1.5099 0.99 7075 362 0.1233 0.1326 REMARK 3 12 1.5099 - 1.4667 0.99 7071 365 0.1266 0.1534 REMARK 3 13 1.4667 - 1.4281 0.99 7052 353 0.1288 0.1268 REMARK 3 14 1.4281 - 1.3933 0.99 7043 371 0.1318 0.1389 REMARK 3 15 1.3933 - 1.3616 0.98 7038 313 0.1343 0.1490 REMARK 3 16 1.3616 - 1.3327 0.98 6936 379 0.1397 0.1582 REMARK 3 17 1.3327 - 1.3060 0.99 6958 401 0.1423 0.1538 REMARK 3 18 1.3060 - 1.2814 0.98 6985 384 0.1426 0.1547 REMARK 3 19 1.2814 - 1.2585 0.98 6942 356 0.1500 0.1701 REMARK 3 20 1.2585 - 1.2372 0.98 6875 359 0.1548 0.1497 REMARK 3 21 1.2372 - 1.2172 0.98 6939 378 0.1591 0.1676 REMARK 3 22 1.2172 - 1.1985 0.98 6937 367 0.1629 0.1671 REMARK 3 23 1.1985 - 1.1809 0.98 6864 363 0.1694 0.1789 REMARK 3 24 1.1809 - 1.1642 0.97 6847 351 0.1693 0.1732 REMARK 3 25 1.1642 - 1.1485 0.96 6832 352 0.1777 0.1865 REMARK 3 26 1.1485 - 1.1336 0.97 6866 358 0.1823 0.1791 REMARK 3 27 1.1336 - 1.1194 0.97 6808 379 0.1920 0.1989 REMARK 3 28 1.1194 - 1.1059 0.95 6683 398 0.1955 0.2048 REMARK 3 29 1.1059 - 1.0931 0.92 6544 313 0.2162 0.2158 REMARK 3 30 1.0931 - 1.0808 0.88 6220 307 0.2324 0.2389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 4140 REMARK 3 ANGLE : 1.496 5688 REMARK 3 CHIRALITY : 0.090 637 REMARK 3 PLANARITY : 0.010 757 REMARK 3 DIHEDRAL : 12.477 1513 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5DGT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213184. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 213422 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.280 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1BFD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% (V/V) PEG400, 0.15 M CACL2, 0.5% REMARK 280 (V/V), MPD, 0.1 M TRISCL (PH 8.5), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.67050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.40100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.67100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.67050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.40100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.67100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.67050 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.40100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 68.67100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.67050 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.40100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 68.67100 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 26970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -233.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 94.80200 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 94.80200 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 MG MG A 601 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 966 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1024 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1030 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1207 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH12 ARG A 120 O HOH A 702 1.26 REMARK 500 HD21 ASN A 455 O HOH A 712 1.51 REMARK 500 O HOH A 712 O HOH A 1205 1.85 REMARK 500 O HOH A 1089 O HOH A 1154 1.85 REMARK 500 O HOH A 758 O HOH A 1225 1.85 REMARK 500 OE2 GLU A 501 O HOH A 701 1.89 REMARK 500 NH1 ARG A 120 O HOH A 702 1.90 REMARK 500 OE1 GLU A 342 O HOH A 703 1.92 REMARK 500 O HOH A 717 O HOH A 721 1.92 REMARK 500 O HOH A 1228 O HOH A 1244 1.94 REMARK 500 O HOH A 1098 O HOH A 1200 1.95 REMARK 500 O HOH A 721 O HOH A 1157 1.95 REMARK 500 O HOH A 714 O HOH A 1323 1.96 REMARK 500 O HOH A 792 O HOH A 1116 1.97 REMARK 500 O HOH A 826 O HOH A 1028 1.97 REMARK 500 OD1 ASP A 347 O HOH A 704 1.98 REMARK 500 OD2 ASP A 18 O HOH A 705 2.01 REMARK 500 O HOH A 980 O HOH A 1163 2.03 REMARK 500 O HOH A 758 O HOH A 1194 2.04 REMARK 500 O HOH A 1366 O HOH A 1370 2.04 REMARK 500 O HOH A 768 O HOH A 1088 2.05 REMARK 500 O HOH A 826 O HOH A 1146 2.05 REMARK 500 O HOH A 1262 O HOH A 1323 2.05 REMARK 500 O HOH A 1076 O HOH A 1080 2.06 REMARK 500 O HOH A 1114 O HOH A 1345 2.08 REMARK 500 O HOH A 714 O HOH A 1122 2.08 REMARK 500 OD1 ASP A 191 O HOH A 706 2.08 REMARK 500 O HOH A 1080 O HOH A 1386 2.09 REMARK 500 O HOH A 704 O HOH A 943 2.09 REMARK 500 O HOH A 1155 O HOH A 1228 2.10 REMARK 500 O HOH A 1078 O HOH A 1337 2.12 REMARK 500 O HOH A 705 O HOH A 813 2.12 REMARK 500 O HOH A 1288 O HOH A 1309 2.12 REMARK 500 O HOH A 1256 O HOH A 1280 2.13 REMARK 500 O HOH A 965 O HOH A 1213 2.13 REMARK 500 O HOH A 815 O HOH A 1206 2.14 REMARK 500 O HOH A 715 O HOH A 873 2.14 REMARK 500 O HOH A 1312 O HOH A 1355 2.15 REMARK 500 OC2 TZD A 605 O HOH A 707 2.16 REMARK 500 O HOH A 842 O HOH A 935 2.17 REMARK 500 O HOH A 1215 O HOH A 1413 2.17 REMARK 500 O HOH A 1323 O HOH A 1410 2.17 REMARK 500 O HOH A 935 O HOH A 1244 2.18 REMARK 500 O HOH A 1042 O HOH A 1309 2.18 REMARK 500 O HOH A 709 O HOH A 711 2.18 REMARK 500 O HOH A 1208 O HOH A 1209 2.19 REMARK 500 O HOH A 1252 O HOH A 1311 2.19 REMARK 500 O HOH A 1164 O HOH A 1276 2.19 REMARK 500 O HOH A 1150 O HOH A 1385 2.19 REMARK 500 OE2 GLU A 509 O HOH A 708 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 701 O HOH A 1088 8555 1.88 REMARK 500 O HOH A 1098 O HOH A 1244 8555 1.93 REMARK 500 O HOH A 719 O HOH A 1428 2565 2.03 REMARK 500 O HOH A 1291 O HOH A 1416 2565 2.08 REMARK 500 O HOH A 1066 O HOH A 1404 8455 2.09 REMARK 500 O HOH A 704 O HOH A 813 8555 2.11 REMARK 500 O HOH A 723 O HOH A 844 8555 2.11 REMARK 500 O HOH A 701 O HOH A 1316 8555 2.15 REMARK 500 O HOH A 907 O HOH A 1117 2565 2.16 REMARK 500 O HOH A 1200 O HOH A 1343 8555 2.18 REMARK 500 O HOH A 701 O HOH A 866 8555 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 71 -146.44 52.10 REMARK 500 SER A 71 -145.32 50.45 REMARK 500 ASN A 202 66.06 -150.03 REMARK 500 HIS A 281 -71.32 -137.66 REMARK 500 ASP A 284 66.62 -154.28 REMARK 500 GLU A 375 47.34 -140.39 REMARK 500 PRO A 447 45.39 -86.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1426 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A1427 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A1428 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A1429 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A1430 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH A1431 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1432 DISTANCE = 6.65 ANGSTROMS REMARK 525 HOH A1433 DISTANCE = 6.72 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 603 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 37 O REMARK 620 2 ASP A 364 OD1 107.1 REMARK 620 3 HOH A 884 O 103.4 3.7 REMARK 620 4 HOH A1070 O 105.7 1.7 2.7 REMARK 620 5 HOH A1212 O 105.7 4.3 5.1 3.1 REMARK 620 6 HOH A1217 O 102.7 5.1 3.2 3.4 3.4 REMARK 620 7 HOH A1245 O 105.1 2.2 1.7 2.1 5.1 4.3 REMARK 620 8 HOH A1368 O 105.5 3.7 4.4 2.4 0.8 2.9 4.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 117 O REMARK 620 2 ASN A 117 O 0.0 REMARK 620 3 LEU A 118 O 75.5 75.5 REMARK 620 4 LEU A 118 O 75.5 75.5 0.0 REMARK 620 5 ARG A 120 O 91.8 91.8 93.7 93.7 REMARK 620 6 ARG A 120 O 91.8 91.8 93.7 93.7 0.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 604 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 347 OD1 REMARK 620 2 ASP A 347 OD2 51.0 REMARK 620 3 ALA A 416 O 33.6 71.7 REMARK 620 4 HOH A 935 O 31.7 69.6 2.2 REMARK 620 5 HOH A1019 O 35.6 72.0 2.6 4.0 REMARK 620 6 HOH A1155 O 34.5 75.1 3.9 5.7 5.6 REMARK 620 7 HOH A1204 O 37.2 75.1 3.8 6.0 3.2 3.9 REMARK 620 8 HOH A1228 O 32.5 73.3 3.5 4.5 5.9 2.0 5.2 REMARK 620 9 HOH A1244 O 30.7 70.8 3.3 2.8 5.8 4.4 6.5 2.5 REMARK 620 N 1 2 3 4 5 6 7 8 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 602 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 428 OD1 REMARK 620 2 ASN A 455 OD1 88.1 REMARK 620 3 THR A 457 O 107.1 86.6 REMARK 620 4 TZD A 605 O13 87.5 175.1 92.7 REMARK 620 5 TZD A 605 O21 165.2 101.4 85.0 83.4 REMARK 620 6 HOH A 770 O 80.5 85.7 169.0 95.6 88.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TZD A 605 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DEI RELATED DB: PDB REMARK 900 RELATED ID: 5DGD RELATED DB: PDB DBREF 5DGT A 2 525 UNP P20906 MDLC_PSEPU 2 525 SEQADV 5DGT ALA A 70 UNP P20906 HIS 70 ENGINEERED MUTATION SEQRES 1 A 524 ALA SER VAL HIS GLY THR THR TYR GLU LEU LEU ARG ARG SEQRES 2 A 524 GLN GLY ILE ASP THR VAL PHE GLY ASN PRO GLY SER ASN SEQRES 3 A 524 GLU LEU PRO PHE LEU LYS ASP PHE PRO GLU ASP PHE ARG SEQRES 4 A 524 TYR ILE LEU ALA LEU GLN GLU ALA CYS VAL VAL GLY ILE SEQRES 5 A 524 ALA ASP GLY TYR ALA GLN ALA SER ARG LYS PRO ALA PHE SEQRES 6 A 524 ILE ASN LEU ALA SER ALA ALA GLY THR GLY ASN ALA MET SEQRES 7 A 524 GLY ALA LEU SER ASN ALA TRP ASN SER HIS SER PRO LEU SEQRES 8 A 524 ILE VAL THR ALA GLY GLN GLN THR ARG ALA MET ILE GLY SEQRES 9 A 524 VAL GLU ALA LEU LEU THR ASN VAL ASP ALA ALA ASN LEU SEQRES 10 A 524 PRO ARG PRO LEU VAL LYS TRP SER TYR GLU PRO ALA SER SEQRES 11 A 524 ALA ALA GLU VAL PRO HIS ALA MET SER ARG ALA ILE HIS SEQRES 12 A 524 MET ALA SER MET ALA PRO GLN GLY PRO VAL TYR LEU SER SEQRES 13 A 524 VAL PRO TYR ASP ASP TRP ASP LYS ASP ALA ASP PRO GLN SEQRES 14 A 524 SER HIS HIS LEU PHE ASP ARG HIS VAL SER SER SER VAL SEQRES 15 A 524 ARG LEU ASN ASP GLN ASP LEU ASP ILE LEU VAL LYS ALA SEQRES 16 A 524 LEU ASN SER ALA SER ASN PRO ALA ILE VAL LEU GLY PRO SEQRES 17 A 524 ASP VAL ASP ALA ALA ASN ALA ASN ALA ASP CYS VAL MET SEQRES 18 A 524 LEU ALA GLU ARG LEU LYS ALA PRO VAL TRP VAL ALA PRO SEQRES 19 A 524 SER ALA PRO ARG CYS PRO PHE PRO THR ARG HIS PRO CYS SEQRES 20 A 524 PHE ARG GLY LEU MET PRO ALA GLY ILE ALA ALA ILE SER SEQRES 21 A 524 GLN LEU LEU GLU GLY HIS ASP VAL VAL LEU VAL ILE GLY SEQRES 22 A 524 ALA PRO VAL PHE ARG TYR HIS GLN TYR ASP PRO GLY GLN SEQRES 23 A 524 TYR LEU LYS PRO GLY THR ARG LEU ILE SER VAL THR CYS SEQRES 24 A 524 ASP PRO LEU GLU ALA ALA ARG ALA PRO MET GLY ASP ALA SEQRES 25 A 524 ILE VAL ALA ASP ILE GLY ALA MET ALA SER ALA LEU ALA SEQRES 26 A 524 ASN LEU VAL GLU GLU SER SER ARG GLN LEU PRO THR ALA SEQRES 27 A 524 ALA PRO GLU PRO ALA LYS VAL ASP GLN ASP ALA GLY ARG SEQRES 28 A 524 LEU HIS PRO GLU THR VAL PHE ASP THR LEU ASN ASP MET SEQRES 29 A 524 ALA PRO GLU ASN ALA ILE TYR LEU ASN GLU SER THR SER SEQRES 30 A 524 THR THR ALA GLN MET TRP GLN ARG LEU ASN MET ARG ASN SEQRES 31 A 524 PRO GLY SER TYR TYR PHE CYS ALA ALA GLY GLY LEU GLY SEQRES 32 A 524 PHE ALA LEU PRO ALA ALA ILE GLY VAL GLN LEU ALA GLU SEQRES 33 A 524 PRO GLU ARG GLN VAL ILE ALA VAL ILE GLY ASP GLY SER SEQRES 34 A 524 ALA ASN TYR SER ILE SER ALA LEU TRP THR ALA ALA GLN SEQRES 35 A 524 TYR ASN ILE PRO THR ILE PHE VAL ILE MET ASN ASN GLY SEQRES 36 A 524 THR TYR GLY ALA LEU ARG TRP PHE ALA GLY VAL LEU GLU SEQRES 37 A 524 ALA GLU ASN VAL PRO GLY LEU ASP VAL PRO GLY ILE ASP SEQRES 38 A 524 PHE ARG ALA LEU ALA LYS GLY TYR GLY VAL GLN ALA LEU SEQRES 39 A 524 LYS ALA ASP ASN LEU GLU GLN LEU LYS GLY SER LEU GLN SEQRES 40 A 524 GLU ALA LEU SER ALA LYS GLY PRO VAL LEU ILE GLU VAL SEQRES 41 A 524 SER THR VAL SER HET MG A 601 1 HET CA A 602 1 HET CA A 603 1 HET CA A 604 1 HET TZD A 605 42 HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION HETNAM TZD 2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL- HETNAM 2 TZD 2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGEN HETNAM 3 TZD DIPHOSPHATE HETSYN TZD THIAMIN THIAZOLONE DIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 CA 3(CA 2+) FORMUL 6 TZD C12 H18 N4 O8 P2 S FORMUL 7 HOH *733(H2 O) HELIX 1 AA1 SER A 3 GLN A 15 1 13 HELIX 2 AA2 GLY A 25 ASN A 27 5 3 HELIX 3 AA3 GLU A 28 LYS A 33 1 6 HELIX 4 AA4 GLN A 46 ARG A 62 1 17 HELIX 5 AA5 ALA A 70 ALA A 78 1 9 HELIX 6 AA6 ALA A 78 SER A 88 1 11 HELIX 7 AA7 THR A 100 GLY A 105 1 6 HELIX 8 AA8 ASP A 114 LEU A 118 5 5 HELIX 9 AA9 SER A 131 ALA A 133 5 3 HELIX 10 AB1 GLU A 134 MET A 148 1 15 HELIX 11 AB2 ASP A 161 TRP A 163 5 3 HELIX 12 AB3 ASP A 168 PHE A 175 5 8 HELIX 13 AB4 ASN A 186 ALA A 200 1 15 HELIX 14 AB5 GLY A 208 ALA A 214 1 7 HELIX 15 AB6 ALA A 216 LYS A 228 1 13 HELIX 16 AB7 GLY A 256 GLU A 265 1 10 HELIX 17 AB8 ASP A 301 ALA A 308 1 8 HELIX 18 AB9 ASP A 317 VAL A 329 1 13 HELIX 19 AC1 HIS A 354 ALA A 366 1 13 HELIX 20 AC2 THR A 379 LEU A 387 1 9 HELIX 21 AC3 PHE A 405 GLU A 417 1 13 HELIX 22 AC4 GLY A 429 TYR A 433 5 5 HELIX 23 AC5 SER A 434 SER A 436 5 3 HELIX 24 AC6 ALA A 437 ASN A 445 1 9 HELIX 25 AC7 TYR A 458 GLU A 469 1 12 HELIX 26 AC8 ASP A 482 GLY A 491 1 10 HELIX 27 AC9 ASN A 499 ALA A 513 1 15 SHEET 1 AA1 6 ARG A 40 LEU A 43 0 SHEET 2 AA1 6 THR A 19 GLY A 22 1 N VAL A 20 O ILE A 42 SHEET 3 AA1 6 ALA A 65 LEU A 69 1 O PHE A 66 N PHE A 21 SHEET 4 AA1 6 LEU A 92 GLN A 98 1 O ILE A 93 N ILE A 67 SHEET 5 AA1 6 VAL A 154 PRO A 159 1 O VAL A 154 N VAL A 94 SHEET 6 AA1 6 SER A 126 TYR A 127 1 N TYR A 127 O SER A 157 SHEET 1 AA2 6 PHE A 249 LEU A 252 0 SHEET 2 AA2 6 VAL A 231 VAL A 233 1 N VAL A 231 O ARG A 250 SHEET 3 AA2 6 ALA A 204 LEU A 207 1 N LEU A 207 O TRP A 232 SHEET 4 AA2 6 VAL A 269 ILE A 273 1 O ILE A 273 N VAL A 206 SHEET 5 AA2 6 ARG A 294 THR A 299 1 O ILE A 296 N VAL A 272 SHEET 6 AA2 6 ASP A 312 VAL A 315 1 O ILE A 314 N THR A 299 SHEET 1 AA3 6 TYR A 395 PHE A 397 0 SHEET 2 AA3 6 ILE A 371 GLU A 375 1 N ASN A 374 O TYR A 396 SHEET 3 AA3 6 VAL A 422 GLY A 427 1 O VAL A 425 N GLU A 375 SHEET 4 AA3 6 ILE A 449 ASN A 454 1 O VAL A 451 N ALA A 424 SHEET 5 AA3 6 VAL A 517 SER A 522 1 O VAL A 521 N ILE A 452 SHEET 6 AA3 6 GLN A 493 ALA A 497 1 N GLN A 493 O LEU A 518 LINK O GLU A 37 CA CA A 603 1555 8455 2.39 LINK O ASN A 117 MG MG A 601 1555 1555 2.69 LINK O ASN A 117 MG MG A 601 1555 2565 2.69 LINK O LEU A 118 MG MG A 601 1555 1555 2.41 LINK O LEU A 118 MG MG A 601 1555 2565 2.41 LINK O ARG A 120 MG MG A 601 1555 1555 2.44 LINK O ARG A 120 MG MG A 601 1555 2565 2.44 LINK OD1 ASP A 347 CA CA A 604 1555 8555 2.69 LINK OD2 ASP A 347 CA CA A 604 1555 8555 2.36 LINK OD1 ASP A 364 CA CA A 603 1555 1555 2.31 LINK O ALA A 416 CA CA A 604 1555 1555 2.30 LINK OD1 ASP A 428 CA CA A 602 1555 1555 2.28 LINK OD1 ASN A 455 CA CA A 602 1555 1555 2.29 LINK O THR A 457 CA CA A 602 1555 1555 2.24 LINK CA CA A 602 O13 TZD A 605 1555 1555 2.22 LINK CA CA A 602 O21 TZD A 605 1555 1555 2.27 LINK CA CA A 602 O HOH A 770 1555 1555 2.25 LINK CA CA A 603 O HOH A 884 1555 1555 2.48 LINK CA CA A 603 O HOH A1070 1555 8555 2.96 LINK CA CA A 603 O HOH A1212 1555 1555 2.49 LINK CA CA A 603 O HOH A1217 1555 1555 2.35 LINK CA CA A 603 O HOH A1245 1555 1555 2.22 LINK CA CA A 603 O HOH A1368 1555 1555 2.39 LINK CA CA A 604 O HOH A 935 1555 1555 2.47 LINK CA CA A 604 O HOH A1019 1555 1555 2.44 LINK CA CA A 604 O HOH A1155 1555 1555 2.70 LINK CA CA A 604 O HOH A1204 1555 1555 2.48 LINK CA CA A 604 O HOH A1228 1555 1555 2.23 LINK CA CA A 604 O HOH A1244 1555 1555 2.69 CISPEP 1 ARG A 120 PRO A 121 0 11.93 CISPEP 2 ALA A 149 PRO A 150 0 -9.85 CISPEP 3 VAL A 277 PHE A 278 0 -21.27 SITE 1 AC1 3 ASN A 117 LEU A 118 ARG A 120 SITE 1 AC2 5 ASP A 428 ASN A 455 THR A 457 TZD A 605 SITE 2 AC2 5 HOH A 770 SITE 1 AC3 8 GLU A 37 ASP A 364 HOH A 884 HOH A1070 SITE 2 AC3 8 HOH A1212 HOH A1217 HOH A1245 HOH A1368 SITE 1 AC4 8 ASP A 347 ALA A 416 HOH A 935 HOH A1019 SITE 2 AC4 8 HOH A1155 HOH A1204 HOH A1228 HOH A1244 SITE 1 AC5 24 ASN A 23 PRO A 24 GLY A 25 GLU A 47 SITE 2 AC5 24 ALA A 70 ASN A 77 THR A 377 SER A 378 SITE 3 AC5 24 GLY A 401 LEU A 403 GLY A 427 ASP A 428 SITE 4 AC5 24 GLY A 429 SER A 430 TYR A 433 ASN A 455 SITE 5 AC5 24 THR A 457 TYR A 458 GLY A 459 ALA A 460 SITE 6 AC5 24 CA A 602 HOH A 707 HOH A 712 HOH A 755 CRYST1 81.341 94.802 137.342 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012294 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007281 0.00000