HEADER LYASE 24-FEB-09 3GDK TITLE CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM TITLE 2 SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: OMP DECARBOXYLASE, OMPDECASE, OMPDCASE, URIDINE 5'- COMPND 5 MONOPHOSPHATE SYNTHASE, UMP SYNTHASE; COMPND 6 EC: 4.1.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: URA3, YEL021W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE, SACCHAROMYCES CEREVISIAE, KEYWDS 2 DECARBOXYLASE, LYASE, PHOSPHOPROTEIN, PYRIMIDINE BIOSYNTHESIS, UBL KEYWDS 3 CONJUGATION EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,B.M.WOOD,J.A.GERLT,S.C.ALMO REVDAT 2 06-SEP-23 3GDK 1 REMARK REVDAT 1 23-JUN-09 3GDK 0 JRNL AUTH K.K.CHAN,B.M.WOOD,A.A.FEDOROV,E.V.FEDOROV,H.J.IMKER, JRNL AUTH 2 T.L.AMYES,J.P.RICHARD,S.C.ALMO,J.A.GERLT JRNL TITL MECHANISM OF THE OROTIDINE 5'-MONOPHOSPHATE JRNL TITL 2 DECARBOXYLASE-CATALYZED REACTION: EVIDENCE FOR SUBSTRATE JRNL TITL 3 DESTABILIZATION. JRNL REF BIOCHEMISTRY V. 48 5518 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19435314 JRNL DOI 10.1021/BI900623R REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2023340.440 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 71799 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 SET) : 0.249 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3627 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6718 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE : 0.3630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 348 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7884 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 426 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 21.58000 REMARK 3 B22 (A**2) : -7.57000 REMARK 3 B33 (A**2) : -14.00000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.23 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.170 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.660 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.790 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 39.40 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : &_1_PARAMETER_INFILE_4 REMARK 3 PARAMETER FILE 5 : &_1_PARAMETER_INFILE_5 REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : &_1_TOPOLOGY_INFILE_4 REMARK 3 TOPOLOGY FILE 5 : &_1_TOPOLOGY_INFILE_5 REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3GDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-07 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 : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 1DQW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1M TRIS-HCL, 0.2M REMARK 280 SODIUM ACETATE, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.0K 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 42.06700 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.55000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.18550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.55000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.06700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.18550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.1 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.6 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C 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 1 REMARK 465 SER A 2 REMARK 465 CYS A 263 REMARK 465 GLY A 264 REMARK 465 GLN A 265 REMARK 465 GLN A 266 REMARK 465 ASN A 267 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 CYS B 263 REMARK 465 GLY B 264 REMARK 465 GLN B 265 REMARK 465 GLN B 266 REMARK 465 ASN B 267 REMARK 465 MET C 1 REMARK 465 SER C 2 REMARK 465 LEU C 206 REMARK 465 ASP C 207 REMARK 465 ASP C 208 REMARK 465 LYS C 209 REMARK 465 GLY C 210 REMARK 465 ASP C 211 REMARK 465 ALA C 212 REMARK 465 LEU C 213 REMARK 465 GLY C 214 REMARK 465 GLN C 215 REMARK 465 GLN C 216 REMARK 465 TYR C 217 REMARK 465 ASN C 267 REMARK 465 MET D 1 REMARK 465 SER D 2 REMARK 465 LEU D 206 REMARK 465 ASP D 207 REMARK 465 ASP D 208 REMARK 465 LYS D 209 REMARK 465 GLY D 210 REMARK 465 ASP D 211 REMARK 465 ALA D 212 REMARK 465 LEU D 213 REMARK 465 GLY D 214 REMARK 465 GLN D 215 REMARK 465 GLN D 216 REMARK 465 TYR D 217 REMARK 465 ASN D 267 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 C 300 O HOH C 405 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 ILE B 183 N - CA - C ANGL. DEV. = -17.3 DEGREES REMARK 500 ILE C 183 N - CA - C ANGL. DEV. = -18.7 DEGREES REMARK 500 ILE D 183 N - CA - C ANGL. DEV. = -18.5 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 ASP A 67 43.78 -142.98 REMARK 500 THR A 73 -61.25 -101.48 REMARK 500 ASN A 85 76.50 63.31 REMARK 500 ARG A 92 112.67 -26.72 REMARK 500 ALA A 95 52.86 -151.39 REMARK 500 ALA A 107 -140.08 -107.25 REMARK 500 ASP A 175 85.85 -156.75 REMARK 500 PHE A 238 -12.18 -143.83 REMARK 500 ASP B 37 79.27 -100.95 REMARK 500 THR B 73 -60.69 -107.12 REMARK 500 ASN B 85 73.85 64.07 REMARK 500 ARG B 92 115.16 -30.25 REMARK 500 ALA B 95 49.21 -150.30 REMARK 500 ALA B 107 -133.11 -113.49 REMARK 500 ASP B 175 87.61 -153.32 REMARK 500 PHE B 238 -12.51 -142.72 REMARK 500 THR C 73 -61.95 -109.55 REMARK 500 ASN C 85 77.78 58.68 REMARK 500 ARG C 92 116.62 -35.42 REMARK 500 ALA C 95 52.24 -150.73 REMARK 500 ALA C 107 -137.56 -110.22 REMARK 500 THR D 73 -64.26 -107.32 REMARK 500 ASN D 85 78.53 56.53 REMARK 500 ARG D 92 115.52 -31.85 REMARK 500 ALA D 95 52.18 -150.36 REMARK 500 ALA D 107 -139.12 -106.42 REMARK 500 ASP D 175 89.09 -160.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DQW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE (THE SAME REMARK 900 PROTEIN WITH DIFFERENT UNIT CELL PARAMETERS) REMARK 900 RELATED ID: 3GDL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH 6-AZAURIDINE 5'- REMARK 900 MONOPHOSPHATE REMARK 900 RELATED ID: 3GDM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE K93R MUTANT OF THE OROTIDINE 5'- REMARK 900 MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE REMARK 900 RELATED ID: 3GDR RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'- REMARK 900 MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE REMARK 900 RELATED ID: 3GDT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'- REMARK 900 MONOPHOSPHATE DECARBOXYLASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED REMARK 900 WITH 6-AZAURIDINE 5'-MONOPHOSPHATE DBREF 3GDK A 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 3GDK B 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 3GDK C 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 3GDK D 1 267 UNP P03962 PYRF_YEAST 1 267 SEQRES 1 A 267 MET SER LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 A 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 A 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 A 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 A 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 A 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 A 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 A 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 A 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 A 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 A 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 A 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 A 267 GLY SER LEU ALA THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 A 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 A 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 A 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 A 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 A 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 A 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 A 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 A 267 ARG ARG CYS GLY GLN GLN ASN SEQRES 1 B 267 MET SER LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 B 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 B 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 B 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 B 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 B 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 B 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 B 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 B 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 B 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 B 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 B 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 B 267 GLY SER LEU ALA THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 B 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 B 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 B 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 B 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 B 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 B 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 B 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 B 267 ARG ARG CYS GLY GLN GLN ASN SEQRES 1 C 267 MET SER LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 C 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 C 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 C 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 C 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 C 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 C 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 C 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 C 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 C 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 C 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 C 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 C 267 GLY SER LEU ALA THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 C 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 C 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 C 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 C 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 C 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 C 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 C 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 C 267 ARG ARG CYS GLY GLN GLN ASN SEQRES 1 D 267 MET SER LYS ALA THR TYR LYS GLU ARG ALA ALA THR HIS SEQRES 2 D 267 PRO SER PRO VAL ALA ALA LYS LEU PHE ASN ILE MET HIS SEQRES 3 D 267 GLU LYS GLN THR ASN LEU CYS ALA SER LEU ASP VAL ARG SEQRES 4 D 267 THR THR LYS GLU LEU LEU GLU LEU VAL GLU ALA LEU GLY SEQRES 5 D 267 PRO LYS ILE CYS LEU LEU LYS THR HIS VAL ASP ILE LEU SEQRES 6 D 267 THR ASP PHE SER MET GLU GLY THR VAL LYS PRO LEU LYS SEQRES 7 D 267 ALA LEU SER ALA LYS TYR ASN PHE LEU LEU PHE GLU ASP SEQRES 8 D 267 ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LEU GLN SEQRES 9 D 267 TYR SER ALA GLY VAL TYR ARG ILE ALA GLU TRP ALA ASP SEQRES 10 D 267 ILE THR ASN ALA HIS GLY VAL VAL GLY PRO GLY ILE VAL SEQRES 11 D 267 SER GLY LEU LYS GLN ALA ALA GLU GLU VAL THR LYS GLU SEQRES 12 D 267 PRO ARG GLY LEU LEU MET LEU ALA GLU LEU SER CYS LYS SEQRES 13 D 267 GLY SER LEU ALA THR GLY GLU TYR THR LYS GLY THR VAL SEQRES 14 D 267 ASP ILE ALA LYS SER ASP LYS ASP PHE VAL ILE GLY PHE SEQRES 15 D 267 ILE ALA GLN ARG ASP MET GLY GLY ARG ASP GLU GLY TYR SEQRES 16 D 267 ASP TRP LEU ILE MET THR PRO GLY VAL GLY LEU ASP ASP SEQRES 17 D 267 LYS GLY ASP ALA LEU GLY GLN GLN TYR ARG THR VAL ASP SEQRES 18 D 267 ASP VAL VAL SER THR GLY SER ASP ILE ILE ILE VAL GLY SEQRES 19 D 267 ARG GLY LEU PHE ALA LYS GLY ARG ASP ALA LYS VAL GLU SEQRES 20 D 267 GLY GLU ARG TYR ARG LYS ALA GLY TRP GLU ALA TYR LEU SEQRES 21 D 267 ARG ARG CYS GLY GLN GLN ASN FORMUL 5 HOH *426(H2 O) HELIX 1 1 THR A 5 HIS A 13 1 9 HELIX 2 2 SER A 15 GLN A 29 1 15 HELIX 3 3 THR A 40 GLY A 52 1 13 HELIX 4 4 PRO A 53 ILE A 55 5 3 HELIX 5 5 HIS A 61 LEU A 65 5 5 HELIX 6 6 THR A 73 ASN A 85 1 13 HELIX 7 7 ILE A 97 ALA A 107 1 11 HELIX 8 8 ARG A 111 TRP A 115 5 5 HELIX 9 9 PRO A 127 THR A 141 1 15 HELIX 10 10 THR A 161 SER A 174 1 14 HELIX 11 11 LEU A 213 TYR A 217 5 5 HELIX 12 12 VAL A 220 THR A 226 1 7 HELIX 13 13 GLY A 234 PHE A 238 5 5 HELIX 14 14 ASP A 243 ARG A 262 1 20 HELIX 15 15 THR B 5 HIS B 13 1 9 HELIX 16 16 SER B 15 GLN B 29 1 15 HELIX 17 17 THR B 40 GLY B 52 1 13 HELIX 18 18 PRO B 53 ILE B 55 5 3 HELIX 19 19 HIS B 61 LEU B 65 5 5 HELIX 20 20 THR B 73 ASN B 85 1 13 HELIX 21 21 ILE B 97 ALA B 107 1 11 HELIX 22 22 ARG B 111 TRP B 115 5 5 HELIX 23 23 PRO B 127 THR B 141 1 15 HELIX 24 24 THR B 161 SER B 174 1 14 HELIX 25 25 GLY B 190 GLY B 194 5 5 HELIX 26 26 LEU B 213 TYR B 217 5 5 HELIX 27 27 VAL B 220 THR B 226 1 7 HELIX 28 28 GLY B 234 PHE B 238 5 5 HELIX 29 29 ASP B 243 ARG B 262 1 20 HELIX 30 30 THR C 5 HIS C 13 1 9 HELIX 31 31 SER C 15 GLN C 29 1 15 HELIX 32 32 THR C 40 GLY C 52 1 13 HELIX 33 33 PRO C 53 ILE C 55 5 3 HELIX 34 34 HIS C 61 LEU C 65 5 5 HELIX 35 35 THR C 73 ASN C 85 1 13 HELIX 36 36 ILE C 97 ALA C 107 1 11 HELIX 37 37 ARG C 111 TRP C 115 5 5 HELIX 38 38 GLY C 123 GLY C 126 5 4 HELIX 39 39 PRO C 127 THR C 141 1 15 HELIX 40 40 GLY C 162 SER C 174 1 13 HELIX 41 41 GLY C 190 GLY C 194 5 5 HELIX 42 42 THR C 219 GLY C 227 1 9 HELIX 43 43 GLY C 234 ALA C 239 1 6 HELIX 44 44 ASP C 243 ARG C 262 1 20 HELIX 45 45 THR D 5 HIS D 13 1 9 HELIX 46 46 SER D 15 GLN D 29 1 15 HELIX 47 47 THR D 40 GLY D 52 1 13 HELIX 48 48 PRO D 53 ILE D 55 5 3 HELIX 49 49 HIS D 61 LEU D 65 5 5 HELIX 50 50 THR D 73 ASN D 85 1 13 HELIX 51 51 ILE D 97 ALA D 107 1 11 HELIX 52 52 ARG D 111 TRP D 115 5 5 HELIX 53 53 GLY D 123 GLY D 126 5 4 HELIX 54 54 PRO D 127 THR D 141 1 15 HELIX 55 55 THR D 161 LYS D 173 1 13 HELIX 56 56 GLY D 190 GLY D 194 5 5 HELIX 57 57 THR D 219 THR D 226 1 8 HELIX 58 58 GLY D 234 ALA D 239 1 6 HELIX 59 59 ASP D 243 ARG D 262 1 20 SHEET 1 A 9 LEU A 32 SER A 35 0 SHEET 2 A 9 LEU A 57 THR A 60 1 O LYS A 59 N ALA A 34 SHEET 3 A 9 LEU A 87 PHE A 94 1 O PHE A 89 N LEU A 58 SHEET 4 A 9 ILE A 118 ALA A 121 1 O ILE A 118 N LEU A 88 SHEET 5 A 9 GLY A 146 LEU A 150 1 O LEU A 150 N ALA A 121 SHEET 6 A 9 VAL A 179 ILE A 183 1 O GLY A 181 N MET A 149 SHEET 7 A 9 LEU A 198 THR A 201 1 O LEU A 198 N PHE A 182 SHEET 8 A 9 ILE A 230 VAL A 233 1 O ILE A 232 N THR A 201 SHEET 9 A 9 LEU A 32 SER A 35 1 N CYS A 33 O ILE A 231 SHEET 1 B 2 VAL A 204 GLY A 205 0 SHEET 2 B 2 ARG A 218 THR A 219 1 O ARG A 218 N GLY A 205 SHEET 1 C 9 LEU B 32 SER B 35 0 SHEET 2 C 9 LEU B 57 THR B 60 1 O LYS B 59 N ALA B 34 SHEET 3 C 9 LEU B 87 PHE B 94 1 O PHE B 89 N LEU B 58 SHEET 4 C 9 ILE B 118 ALA B 121 1 O ILE B 118 N LEU B 88 SHEET 5 C 9 GLY B 146 LEU B 150 1 O LEU B 150 N ALA B 121 SHEET 6 C 9 VAL B 179 ILE B 183 1 O GLY B 181 N MET B 149 SHEET 7 C 9 LEU B 198 THR B 201 1 O MET B 200 N PHE B 182 SHEET 8 C 9 ILE B 230 VAL B 233 1 O ILE B 232 N THR B 201 SHEET 9 C 9 LEU B 32 SER B 35 1 N SER B 35 O VAL B 233 SHEET 1 D 2 VAL B 204 GLY B 205 0 SHEET 2 D 2 ARG B 218 THR B 219 1 O ARG B 218 N GLY B 205 SHEET 1 E 9 LEU C 32 SER C 35 0 SHEET 2 E 9 LEU C 57 THR C 60 1 O LYS C 59 N ALA C 34 SHEET 3 E 9 LEU C 87 PHE C 94 1 O ASP C 91 N THR C 60 SHEET 4 E 9 ILE C 118 ALA C 121 1 O ILE C 118 N LEU C 88 SHEET 5 E 9 GLY C 146 LEU C 150 1 O LEU C 150 N ALA C 121 SHEET 6 E 9 VAL C 179 ILE C 183 1 O GLY C 181 N MET C 149 SHEET 7 E 9 LEU C 198 THR C 201 1 O LEU C 198 N ILE C 180 SHEET 8 E 9 ILE C 230 VAL C 233 1 O ILE C 230 N THR C 201 SHEET 9 E 9 LEU C 32 SER C 35 1 N CYS C 33 O ILE C 231 SHEET 1 F 9 LEU D 32 SER D 35 0 SHEET 2 F 9 LEU D 57 THR D 60 1 O LYS D 59 N ALA D 34 SHEET 3 F 9 LEU D 87 PHE D 94 1 O PHE D 89 N LEU D 58 SHEET 4 F 9 ILE D 118 ALA D 121 1 O ILE D 118 N LEU D 88 SHEET 5 F 9 GLY D 146 LEU D 150 1 O LEU D 150 N ALA D 121 SHEET 6 F 9 VAL D 179 ILE D 183 1 O GLY D 181 N MET D 149 SHEET 7 F 9 LEU D 198 THR D 201 1 O LEU D 198 N ILE D 180 SHEET 8 F 9 ILE D 230 VAL D 233 1 O ILE D 232 N THR D 201 SHEET 9 F 9 LEU D 32 SER D 35 1 N CYS D 33 O ILE D 231 CRYST1 84.134 98.371 127.100 90.00 90.00 90.00 P 21 21 21 16 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 0.011886 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007868 0.00000