HEADER LYASE 10-JUN-07 2V30 TITLE HUMAN OROTIDINE 5'-PHOSPHATE DECARBOXYLASE DOMAIN OF URIDINE TITLE 2 MONOPHOSPATE SYNTHETASE (UMPS) IN COMPLEX WITH ITS PRODUCT UMP. COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE DOMAIN, RESIDUES 224- COMPND 5 479; COMPND 6 SYNONYM: OMPDECASE, URIDINE MONOPHOSPHATE SYNTHETASE-UMPS; COMPND 7 EC: 4.1.1.23; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC-BSA4; SOURCE 9 OTHER_DETAILS: MAMMALIAN GENE COLLECTION (MGC) KEYWDS ALTERNATIVE SPLICING, PYRIMIDINE METABOLISM, DISEASE MUTATION, KEYWDS 2 GLYCOSYLTRANSFERASE, UMP, LYASE, TRANSFERASE, POLYMORPHISM, KEYWDS 3 DECARBOXYLASE, MULTIFUNCTIONAL ENZYME, PYRIMIDINE BIOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR M.MOCHE,D.OGG,C.ARROWSMITH,H.BERGLUND,R.BUSAM,R.COLLINS,L.G.DAHLGREN, AUTHOR 2 A.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND,M.HAMMARSTROM,B.M.HALLBERG, AUTHOR 3 L.HOLMBERG-SCHIAVONE,I.JOHANSSON,A.KALLAS,T.KARLBERG,T.KOTENYOVA, AUTHOR 4 L.LEHTIO,T.NYMAN,C.PERSSON,J.SAGEMARK,P.STENMARK,M.SUNDSTROM, AUTHOR 5 A.G.THORSELL,S.VAN DEN BERG,J.WEIGELT,M.WELIN,P.NORDLUND,STRUCTURAL AUTHOR 6 GENOMICS CONSORTIUM (SGC) REVDAT 4 13-DEC-23 2V30 1 REMARK REVDAT 3 13-DEC-17 2V30 1 AUTHOR JRNL REVDAT 2 24-FEB-09 2V30 1 VERSN REVDAT 1 24-JUL-07 2V30 0 JRNL AUTH M.MOCHE,D.OGG,C.ARROWSMITH,H.BERGLUND,R.BUSAM,R.COLLINS, JRNL AUTH 2 L.G.DAHLGREN,A.EDWARDS,S.FLODIN,A.FLORES,S.GRASLUND, JRNL AUTH 3 M.HAMMARSTROM,B.M.HALLBERG,L.HOLMBERG-SCHIAVONE,I.JOHANSSON, JRNL AUTH 4 A.KALLAS,T.KARLBERG,T.KOTENYOVA,L.LEHTIO,T.NYMAN,C.PERSSON, JRNL AUTH 5 J.SAGEMARK,P.STENMARK,M.SUNDSTROM,A.G.THORSELL, JRNL AUTH 6 S.VAN DEN BERG,J.WEIGELT,M.WELIN,P.NORDLUND JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-DECARBOXYLASE JRNL TITL 2 DOMAIN OF HUMAN URIDINE MONOPHOSPHATE SYNTHETASE (UMPS) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 46851 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2482 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3385 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1770 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 574 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : 1.59000 REMARK 3 B33 (A**2) : -1.10000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.131 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.077 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.688 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4345 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2986 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5903 ; 1.338 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7309 ; 0.949 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 570 ; 6.016 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;35.914 ;23.520 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 793 ;13.311 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;12.577 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 666 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4928 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 882 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 908 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3293 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2137 ; 0.166 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2233 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 490 ; 0.176 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 10 ; 0.209 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 41 ; 0.316 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.170 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3565 ; 1.444 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4390 ; 1.590 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1838 ; 2.637 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1513 ; 3.568 ; 5.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2V30 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1290032859. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00595 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49400 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.10 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 35.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2JGY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 30.05150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.60450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.92650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.60450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.05150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.92650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 201 REMARK 465 HIS A 202 REMARK 465 HIS A 203 REMARK 465 HIS A 204 REMARK 465 HIS A 205 REMARK 465 HIS A 206 REMARK 465 HIS A 207 REMARK 465 SER A 208 REMARK 465 SER A 209 REMARK 465 GLY A 210 REMARK 465 VAL A 211 REMARK 465 ASP A 212 REMARK 465 LEU A 213 REMARK 465 GLY A 214 REMARK 465 THR A 215 REMARK 465 GLU A 216 REMARK 465 ASN A 217 REMARK 465 MET B 201 REMARK 465 HIS B 202 REMARK 465 HIS B 203 REMARK 465 HIS B 204 REMARK 465 HIS B 205 REMARK 465 HIS B 206 REMARK 465 HIS B 207 REMARK 465 SER B 208 REMARK 465 SER B 209 REMARK 465 GLY B 210 REMARK 465 VAL B 211 REMARK 465 ASP B 212 REMARK 465 LEU B 213 REMARK 465 GLY B 214 REMARK 465 THR B 215 REMARK 465 GLU B 216 REMARK 465 ASN B 217 REMARK 465 LEU B 218 REMARK 465 TYR B 219 REMARK 465 PHE B 220 REMARK 465 GLN B 221 REMARK 465 SER B 222 REMARK 465 GLY B 479 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 O HOH A 2011 O HOH A 2013 1.96 REMARK 500 OE2 GLU B 306 O HOH B 2079 2.03 REMARK 500 O HOH B 2242 O HOH B 2243 2.04 REMARK 500 O HOH A 2025 O HOH A 2092 2.08 REMARK 500 O HOH B 2156 O HOH B 2218 2.17 REMARK 500 O LYS B 250 O HOH B 2021 2.18 REMARK 500 O HOH A 2163 O HOH A 2256 2.18 REMARK 500 OE2 GLU B 297 O HOH B 2068 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 388 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES 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 GLU A 306 74.71 66.34 REMARK 500 ALA A 316 37.18 -158.51 REMARK 500 GLU B 306 72.81 68.32 REMARK 500 GLU B 306 75.09 71.28 REMARK 500 ALA B 316 38.64 -159.14 REMARK 500 PHE B 396 -45.89 -130.12 REMARK 500 ASP B 426 -169.95 -115.68 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 A2140 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH B2094 DISTANCE = 7.69 ANGSTROMS REMARK 525 HOH B2131 DISTANCE = 6.82 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A1480 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B1479 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JGY RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN OROTIDINE-5 '-DECARBOXYLASE DOMAIN REMARK 900 OF HUMAN URIDINE MONOPHOSPHATE SYNTHETASE (UMPS) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT CONTAINS A HEXAHISTIDINE TAG AND A LINKER REMARK 999 SEQUENCE IN THE N-TERMINUS. THE CONSTRUCT OF THE C- REMARK 999 TERMINAL DOMAIN OF UMPS CALLED ORITIDINE 5'-PHOSPHATE REMARK 999 DECARBOXYLASE DOMAIN CONTAIN GLU224-G479 IN UMPS (P11172). DBREF 2V30 A 201 223 PDB 2V30 2V30 201 223 DBREF 2V30 A 224 479 UNP P11172 PYR5_HUMAN 224 479 DBREF 2V30 B 201 223 PDB 2V30 2V30 201 223 DBREF 2V30 B 224 479 UNP P11172 PYR5_HUMAN 224 479 SEQRES 1 A 279 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 279 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLU LEU SER SEQRES 3 A 279 PHE GLY ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL SEQRES 4 A 279 ALA SER LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR SEQRES 5 A 279 ASN LEU CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU SEQRES 6 A 279 LEU LEU GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS SEQRES 7 A 279 MET LEU LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR SEQRES 8 A 279 LEU ASP VAL MET LYS GLU LEU ILE THR LEU ALA LYS CYS SEQRES 9 A 279 HIS GLU PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP SEQRES 10 A 279 ILE GLY ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE SEQRES 11 A 279 PHE LYS ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS SEQRES 12 A 279 VAL VAL PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU SEQRES 13 A 279 VAL GLY LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA SEQRES 14 A 279 GLU MET SER SER THR GLY SER LEU ALA THR GLY ASP TYR SEQRES 15 A 279 THR ARG ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU SEQRES 16 A 279 PHE VAL VAL GLY PHE ILE SER GLY SER ARG VAL SER MET SEQRES 17 A 279 LYS PRO GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU SEQRES 18 A 279 GLU ALA GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER SEQRES 19 A 279 PRO GLN GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE SEQRES 20 A 279 ILE VAL GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU SEQRES 21 A 279 GLU ALA ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA SEQRES 22 A 279 TYR LEU SER ARG LEU GLY SEQRES 1 B 279 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 B 279 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLU LEU SER SEQRES 3 B 279 PHE GLY ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL SEQRES 4 B 279 ALA SER LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR SEQRES 5 B 279 ASN LEU CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU SEQRES 6 B 279 LEU LEU GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS SEQRES 7 B 279 MET LEU LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR SEQRES 8 B 279 LEU ASP VAL MET LYS GLU LEU ILE THR LEU ALA LYS CYS SEQRES 9 B 279 HIS GLU PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP SEQRES 10 B 279 ILE GLY ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE SEQRES 11 B 279 PHE LYS ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS SEQRES 12 B 279 VAL VAL PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU SEQRES 13 B 279 VAL GLY LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA SEQRES 14 B 279 GLU MET SER SER THR GLY SER LEU ALA THR GLY ASP TYR SEQRES 15 B 279 THR ARG ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU SEQRES 16 B 279 PHE VAL VAL GLY PHE ILE SER GLY SER ARG VAL SER MET SEQRES 17 B 279 LYS PRO GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU SEQRES 18 B 279 GLU ALA GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER SEQRES 19 B 279 PRO GLN GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE SEQRES 20 B 279 ILE VAL GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU SEQRES 21 B 279 GLU ALA ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA SEQRES 22 B 279 TYR LEU SER ARG LEU GLY HET U5P A1480 21 HET U5P B1479 21 HETNAM U5P URIDINE-5'-MONOPHOSPHATE FORMUL 3 U5P 2(C9 H13 N2 O9 P) FORMUL 5 HOH *574(H2 O) HELIX 1 1 SER A 226 GLU A 232 1 7 HELIX 2 2 HIS A 237 GLU A 251 1 15 HELIX 3 3 LEU A 262 GLY A 274 1 13 HELIX 4 4 PRO A 275 ILE A 277 5 3 HELIX 5 5 HIS A 283 LEU A 287 5 5 HELIX 6 6 THR A 291 GLU A 306 1 16 HELIX 7 7 ILE A 318 GLY A 328 1 11 HELIX 8 8 LYS A 332 TRP A 336 5 5 HELIX 9 9 SER A 348 LEU A 359 1 12 HELIX 10 10 THR A 379 HIS A 393 1 15 HELIX 11 11 SER A 434 LYS A 441 1 8 HELIX 12 12 GLY A 450 SER A 455 1 6 HELIX 13 13 ASP A 458 ARG A 477 1 20 HELIX 14 14 SER B 226 GLU B 232 1 7 HELIX 15 15 HIS B 237 GLU B 251 1 15 HELIX 16 16 LEU B 262 GLY B 274 1 13 HELIX 17 17 PRO B 275 ILE B 277 5 3 HELIX 18 18 HIS B 283 LEU B 287 5 5 HELIX 19 19 THR B 291 GLU B 306 1 16 HELIX 20 20 ILE B 318 GLY B 328 1 11 HELIX 21 21 LYS B 332 TRP B 336 5 5 HELIX 22 22 SER B 348 LEU B 359 1 12 HELIX 23 23 THR B 379 GLU B 392 1 14 HELIX 24 24 SER B 434 GLY B 440 1 7 HELIX 25 25 GLY B 450 SER B 455 1 6 HELIX 26 26 ASP B 458 LEU B 478 1 21 SHEET 1 AA10 LEU A 254 SER A 257 0 SHEET 2 AA10 ILE A 446 VAL A 449 1 O ILE A 447 N CYS A 255 SHEET 3 AA10 LEU A 413 THR A 416 1 O HIS A 414 N ILE A 446 SHEET 4 AA10 VAL A 397 ILE A 401 1 O VAL A 398 N LEU A 413 SHEET 5 AA10 GLY A 364 ILE A 368 1 O CYS A 365 N VAL A 398 SHEET 6 AA10 LEU A 339 HIS A 343 1 O VAL A 340 N LEU A 366 SHEET 7 AA10 LEU A 308 PHE A 315 1 O ILE A 309 N LEU A 339 SHEET 8 AA10 MET A 279 THR A 282 1 O LEU A 280 N PHE A 310 SHEET 9 AA10 LEU A 254 SER A 257 1 O LEU A 256 N LYS A 281 SHEET 10 AA10 LEU A 254 SER A 257 0 SHEET 1 AB 2 GLY A 424 GLY A 425 0 SHEET 2 AB 2 GLN A 431 TYR A 432 -1 O TYR A 432 N GLY A 424 SHEET 1 BA 9 LEU B 254 SER B 257 0 SHEET 2 BA 9 ILE B 446 VAL B 449 1 O ILE B 447 N CYS B 255 SHEET 3 BA 9 LEU B 413 THR B 416 1 O HIS B 414 N ILE B 446 SHEET 4 BA 9 VAL B 397 ILE B 401 1 O VAL B 398 N LEU B 413 SHEET 5 BA 9 GLY B 364 ILE B 368 1 O CYS B 365 N VAL B 398 SHEET 6 BA 9 LEU B 339 HIS B 343 1 O VAL B 340 N LEU B 366 SHEET 7 BA 9 LEU B 308 PHE B 315 1 O ILE B 309 N LEU B 339 SHEET 8 BA 9 MET B 279 THR B 282 1 O LEU B 280 N PHE B 310 SHEET 9 BA 9 LEU B 254 SER B 257 1 O LEU B 256 N LYS B 281 SHEET 1 BB 2 GLY B 424 GLY B 425 0 SHEET 2 BB 2 GLN B 431 TYR B 432 -1 O TYR B 432 N GLY B 424 CISPEP 1 LEU A 478 GLY A 479 0 16.03 SITE 1 AC1 19 SER A 257 ASP A 259 LYS A 281 HIS A 283 SITE 2 AC1 19 ASP A 312 LYS A 314 MET A 371 SER A 372 SITE 3 AC1 19 PRO A 417 GLN A 430 TYR A 432 GLY A 450 SITE 4 AC1 19 ARG A 451 HOH A2048 HOH A2320 HOH A2321 SITE 5 AC1 19 ASP B 317 ILE B 318 THR B 321 SITE 1 AC2 20 ASP A 317 ILE A 318 THR A 321 SER B 257 SITE 2 AC2 20 ASP B 259 LYS B 281 HIS B 283 ASP B 312 SITE 3 AC2 20 LYS B 314 MET B 371 SER B 372 PRO B 417 SITE 4 AC2 20 GLN B 430 TYR B 432 GLY B 450 ARG B 451 SITE 5 AC2 20 HOH B2026 HOH B2151 HOH B2252 HOH B2253 CRYST1 60.103 77.853 153.209 90.00 90.00 90.00 P 21 21 21 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 0.016638 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006527 0.00000 MTRIX1 1 0.842600 0.079930 -0.532600 10.40000 1 MTRIX2 1 0.083740 -0.996300 -0.017040 102.60000 1 MTRIX3 1 -0.532000 -0.030240 -0.846200 51.75000 1