HEADER LYASE 24-FEB-09 3GDR TITLE CRYSTAL STRUCTURE OF THE D91N MUTANT OF THE OROTIDINE 5'-MONOPHOSPHATE TITLE 2 DECARBOXYLASE FROM 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; COMPND 8 MUTATION: 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 D91N MUTANT, DECARBOXYLASE, LYASE, PHOSPHOPROTEIN, PYRIMIDINE KEYWDS 3 BIOSYNTHESIS, UBL CONJUGATION EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,B.M.WOOD,J.A.GERLT,S.C.ALMO REVDAT 3 06-SEP-23 3GDR 1 REMARK REVDAT 2 20-OCT-21 3GDR 1 SEQADV REVDAT 1 23-JUN-09 3GDR 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1828484.090 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 83436 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) : 0.252 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4149 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7827 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE : 0.3100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 427 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 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 : 484 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 14.62000 REMARK 3 B22 (A**2) : -6.99000 REMARK 3 B33 (A**2) : -7.63000 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.730 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) : 1.130 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.640 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.030 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.860 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 41.68 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 3GDR 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_1000051733. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 83436 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07400 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 3GDK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M BIS-TRIS, 0.2M REMARK 280 SODIUM CHLORIDE, PH 6.5, 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 42.06100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.32450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.57250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.32450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.06100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.57250 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: 2340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.8 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: 2360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.4 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: 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 A 183 N - CA - C ANGL. DEV. = -16.5 DEGREES REMARK 500 ILE B 183 N - CA - C ANGL. DEV. = -17.1 DEGREES REMARK 500 ILE C 183 N - CA - C ANGL. DEV. = -17.3 DEGREES REMARK 500 ILE D 183 N - CA - C ANGL. DEV. = -17.4 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 37 69.36 -105.36 REMARK 500 ASN A 85 74.15 67.08 REMARK 500 ARG A 92 110.86 -23.72 REMARK 500 ALA A 95 52.01 -153.21 REMARK 500 ALA A 107 -144.79 -117.26 REMARK 500 ARG A 111 50.26 39.39 REMARK 500 ASP A 175 91.82 -160.87 REMARK 500 PHE A 238 -18.01 -145.02 REMARK 500 ASP B 37 72.04 -105.54 REMARK 500 ASN B 85 75.79 60.58 REMARK 500 ARG B 92 109.70 -26.46 REMARK 500 ALA B 95 51.02 -153.43 REMARK 500 ALA B 107 -145.68 -113.81 REMARK 500 ARG B 111 52.36 37.25 REMARK 500 ASP B 175 90.69 -161.04 REMARK 500 PHE B 238 -19.75 -140.26 REMARK 500 ASN C 85 75.08 59.12 REMARK 500 ARG C 92 113.45 -31.29 REMARK 500 ALA C 95 48.32 -150.59 REMARK 500 ALA C 107 -147.75 -109.40 REMARK 500 ASP D 37 72.68 -102.18 REMARK 500 ASN D 85 77.11 60.69 REMARK 500 ARG D 92 110.36 -32.07 REMARK 500 ALA D 95 48.54 -150.69 REMARK 500 ALA D 107 -146.54 -109.61 REMARK 500 ARG D 111 52.65 39.73 REMARK 500 ASP D 175 89.23 -157.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GDK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 FROM SACCHAROMYCES CEREVISIAE (THE SAME PROTEIN IN WT FORM) 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: 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 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) DBREF 3GDR A 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 3GDR B 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 3GDR C 1 267 UNP P03962 PYRF_YEAST 1 267 DBREF 3GDR D 1 267 UNP P03962 PYRF_YEAST 1 267 SEQADV 3GDR ASN A 91 UNP P03962 ASP 91 ENGINEERED MUTATION SEQADV 3GDR ASN B 91 UNP P03962 ASP 91 ENGINEERED MUTATION SEQADV 3GDR ASN C 91 UNP P03962 ASP 91 ENGINEERED MUTATION SEQADV 3GDR ASN D 91 UNP P03962 ASP 91 ENGINEERED MUTATION 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 ASN 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 ASN 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 ASN 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 ASN 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 *484(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 GLY A 190 GLY A 194 5 5 HELIX 12 12 LEU A 213 TYR A 217 5 5 HELIX 13 13 VAL A 220 GLY A 227 1 8 HELIX 14 14 GLY A 234 PHE A 238 5 5 HELIX 15 15 ASP A 243 ARG A 262 1 20 HELIX 16 16 THR B 5 HIS B 13 1 9 HELIX 17 17 SER B 15 GLN B 29 1 15 HELIX 18 18 THR B 40 GLY B 52 1 13 HELIX 19 19 PRO B 53 ILE B 55 5 3 HELIX 20 20 HIS B 61 LEU B 65 5 5 HELIX 21 21 THR B 73 ASN B 85 1 13 HELIX 22 22 ILE B 97 ALA B 107 1 11 HELIX 23 23 ARG B 111 TRP B 115 5 5 HELIX 24 24 GLY B 123 GLY B 126 5 4 HELIX 25 25 PRO B 127 THR B 141 1 15 HELIX 26 26 THR B 161 SER B 174 1 14 HELIX 27 27 GLY B 190 GLY B 194 5 5 HELIX 28 28 LEU B 213 TYR B 217 5 5 HELIX 29 29 VAL B 220 THR B 226 1 7 HELIX 30 30 GLY B 234 PHE B 238 5 5 HELIX 31 31 ASP B 243 ARG B 262 1 20 HELIX 32 32 THR C 5 HIS C 13 1 9 HELIX 33 33 SER C 15 GLN C 29 1 15 HELIX 34 34 THR C 40 GLY C 52 1 13 HELIX 35 35 PRO C 53 ILE C 55 5 3 HELIX 36 36 HIS C 61 LEU C 65 5 5 HELIX 37 37 THR C 73 ASN C 85 1 13 HELIX 38 38 ILE C 97 ALA C 107 1 11 HELIX 39 39 ARG C 111 TRP C 115 5 5 HELIX 40 40 GLY C 123 GLY C 126 5 4 HELIX 41 41 PRO C 127 THR C 141 1 15 HELIX 42 42 GLY C 162 LYS C 173 1 12 HELIX 43 43 GLY C 190 GLY C 194 5 5 HELIX 44 44 THR C 219 GLY C 227 1 9 HELIX 45 45 ASP C 243 ARG C 262 1 20 HELIX 46 46 THR D 5 HIS D 13 1 9 HELIX 47 47 SER D 15 GLN D 29 1 15 HELIX 48 48 THR D 40 GLY D 52 1 13 HELIX 49 49 PRO D 53 ILE D 55 5 3 HELIX 50 50 HIS D 61 LEU D 65 5 5 HELIX 51 51 THR D 73 ASN D 85 1 13 HELIX 52 52 ILE D 97 ALA D 107 1 11 HELIX 53 53 ARG D 111 TRP D 115 5 5 HELIX 54 54 GLY D 123 GLY D 126 5 4 HELIX 55 55 PRO D 127 THR D 141 1 15 HELIX 56 56 THR D 161 LYS D 173 1 13 HELIX 57 57 GLY D 190 GLY D 194 5 5 HELIX 58 58 THR D 219 THR D 226 1 8 HELIX 59 59 GLY D 234 PHE D 238 5 5 HELIX 60 60 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 ILE A 180 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 SER A 35 O VAL A 233 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 PHE C 89 N LEU C 58 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 148 N THR D 119 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 84.122 99.145 126.649 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 0.011887 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007896 0.00000