HEADER LYASE 09-APR-10 3MI2 TITLE CRYSTAL STRUCTURE OF HUMAN OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE TITLE 2 COMPLEXED WITH PYRAZOFURIN MONOPHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN (UNP COMPND 5 RESIDUES 223-480); COMPND 6 SYNONYM: UMP SYNTHASE, OROTATE PHOSPHORIBOSYLTRANSFERASE, OPRTASE, COMPND 7 OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, OMPDECASE; COMPND 8 EC: 4.1.1.23; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GI|13960142, OK/SW-CL.21, UMPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS UMP SYNTHASE, OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE, PYRAZOFURIN KEYWDS 2 MONOPHOSPHATE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,T.TO,L.P.KOTRA,E.F.PAI REVDAT 4 06-SEP-23 3MI2 1 REMARK SEQADV LINK REVDAT 3 12-NOV-14 3MI2 1 HETATM HETNAM VERSN REVDAT 2 16-JUN-10 3MI2 1 JRNL REVDAT 1 26-MAY-10 3MI2 0 JRNL AUTH M.E.MEZA-AVINA,L.WEI,Y.LIU,E.PODUCH,A.M.BELLO,R.K.MISHRA, JRNL AUTH 2 E.F.PAI,L.P.KOTRA JRNL TITL STRUCTURAL DETERMINANTS FOR THE INHIBITORY LIGANDS OF JRNL TITL 2 OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE. JRNL REF BIOORG.MED.CHEM. V. 18 4032 2010 JRNL REFN ISSN 0968-0896 JRNL PMID 20452222 JRNL DOI 10.1016/J.BMC.2010.04.017 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 84.0 REMARK 3 NUMBER OF REFLECTIONS : 140506 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7408 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5482 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 44.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE SET COUNT : 312 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3938 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 692 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.73000 REMARK 3 B22 (A**2) : -0.46000 REMARK 3 B33 (A**2) : 0.70000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.047 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.032 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.720 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4475 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6102 ; 1.519 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 600 ; 6.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;34.061 ;23.989 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 826 ;12.572 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;14.561 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 683 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3409 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2806 ; 0.717 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4548 ; 1.311 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1669 ; 2.213 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1554 ; 3.619 ; 4.500 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 : 1.40 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 3MI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DCM WITH CRYO-COOLED 1ST CRYSTAL REMARK 200 SAGITTALLY BENT 2ND CRYSTAL REMARK 200 FOLLOWED BY VERTICALLY FOCUSING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 147972 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 65.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 84.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.28800 REMARK 200 R SYM FOR SHELL (I) : 0.28800 REMARK 200 FOR SHELL : 2.560 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: 2P1F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 8.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.05450 REMARK 290 SMTRY3 2 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL 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 13 REMARK 465 GLY A 14 REMARK 465 SER A 15 REMARK 465 SER A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 HIS A 22 REMARK 465 SER A 23 REMARK 465 SER A 24 REMARK 465 GLY A 25 REMARK 465 LEU A 26 REMARK 465 VAL A 27 REMARK 465 PRO A 28 REMARK 465 ARG A 29 REMARK 465 GLY A 30 REMARK 465 SER A 31 REMARK 465 HIS A 32 REMARK 465 MET A 33 REMARK 465 VAL A 291 REMARK 465 MET B 13 REMARK 465 GLY B 14 REMARK 465 SER B 15 REMARK 465 SER B 16 REMARK 465 HIS B 17 REMARK 465 HIS B 18 REMARK 465 HIS B 19 REMARK 465 HIS B 20 REMARK 465 HIS B 21 REMARK 465 HIS B 22 REMARK 465 SER B 23 REMARK 465 SER B 24 REMARK 465 GLY B 25 REMARK 465 LEU B 26 REMARK 465 VAL B 27 REMARK 465 PRO B 28 REMARK 465 ARG B 29 REMARK 465 GLY B 30 REMARK 465 SER B 31 REMARK 465 HIS B 32 REMARK 465 MET B 33 REMARK 465 VAL B 291 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 117 74.77 66.27 REMARK 500 ALA A 127 28.54 -160.03 REMARK 500 PHE A 207 -41.36 -131.68 REMARK 500 GLU B 117 74.67 65.47 REMARK 500 ALA B 127 30.76 -159.77 REMARK 500 PHE B 207 -40.56 -132.97 REMARK 500 PHE B 207 -40.56 -132.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFU B 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PFU A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2EAW RELATED DB: PDB REMARK 900 HUMAN UMP SYNTHASE(C-TERMINAL DOMAIN-OROTIDINE 5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE) REMARK 900 RELATED ID: 2P1F RELATED DB: PDB REMARK 900 HUMAN UMP SYNTHASE(C-TERMINAL DOMAIN-OROTIDINE 5'-MONOPHOSPHATE REMARK 900 DECARBOXYLASE) REMARK 900 RELATED ID: 3BGG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COMPLEX WITH BMP REMARK 900 RELATED ID: 3BGJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COVALENTLY MODIFIED BY 6-IODO-UMP REMARK 900 RELATED ID: 3G3D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COVALENTLY MODIFIED BY 5-FLURO-6-AZIDO-UMP REMARK 900 RELATED ID: 3BKO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COMPLEX WITH 5-CN-UMP REMARK 900 RELATED ID: 3BVJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COMPLEX WITH XMP REMARK 900 RELATED ID: 3G3M RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COVALENTLY MODIFIED BY 5-FLURO-6-IODO-UMP DBREF 3MI2 A 34 291 UNP P11172 PYR5_HUMAN 223 480 DBREF 3MI2 B 34 291 UNP P11172 PYR5_HUMAN 223 480 SEQADV 3MI2 MET A 13 UNP P11172 EXPRESSION TAG SEQADV 3MI2 GLY A 14 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER A 15 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER A 16 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 17 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 18 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 19 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 20 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 21 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 22 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER A 23 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER A 24 UNP P11172 EXPRESSION TAG SEQADV 3MI2 GLY A 25 UNP P11172 EXPRESSION TAG SEQADV 3MI2 LEU A 26 UNP P11172 EXPRESSION TAG SEQADV 3MI2 VAL A 27 UNP P11172 EXPRESSION TAG SEQADV 3MI2 PRO A 28 UNP P11172 EXPRESSION TAG SEQADV 3MI2 ARG A 29 UNP P11172 EXPRESSION TAG SEQADV 3MI2 GLY A 30 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER A 31 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS A 32 UNP P11172 EXPRESSION TAG SEQADV 3MI2 MET A 33 UNP P11172 EXPRESSION TAG SEQADV 3MI2 MET B 13 UNP P11172 EXPRESSION TAG SEQADV 3MI2 GLY B 14 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER B 15 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER B 16 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 17 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 18 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 19 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 20 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 21 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 22 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER B 23 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER B 24 UNP P11172 EXPRESSION TAG SEQADV 3MI2 GLY B 25 UNP P11172 EXPRESSION TAG SEQADV 3MI2 LEU B 26 UNP P11172 EXPRESSION TAG SEQADV 3MI2 VAL B 27 UNP P11172 EXPRESSION TAG SEQADV 3MI2 PRO B 28 UNP P11172 EXPRESSION TAG SEQADV 3MI2 ARG B 29 UNP P11172 EXPRESSION TAG SEQADV 3MI2 GLY B 30 UNP P11172 EXPRESSION TAG SEQADV 3MI2 SER B 31 UNP P11172 EXPRESSION TAG SEQADV 3MI2 HIS B 32 UNP P11172 EXPRESSION TAG SEQADV 3MI2 MET B 33 UNP P11172 EXPRESSION TAG SEQRES 1 A 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 279 LEU VAL PRO ARG GLY SER HIS MET LYS GLU LEU SER PHE SEQRES 3 A 279 GLY ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL ALA SEQRES 4 A 279 SER LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR ASN SEQRES 5 A 279 LEU CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU LEU SEQRES 6 A 279 LEU GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS MET SEQRES 7 A 279 LEU LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR LEU SEQRES 8 A 279 ASP VAL MET LYS GLU LEU ILE THR LEU ALA LYS CSD HIS SEQRES 9 A 279 GLU PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP ILE SEQRES 10 A 279 GLY ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE PHE SEQRES 11 A 279 LYS ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS VAL SEQRES 12 A 279 VAL PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU VAL SEQRES 13 A 279 GLY LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA GLU SEQRES 14 A 279 MET SER SER THR GLY SER LEU ALA THR GLY ASP TYR THR SEQRES 15 A 279 ARG ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU PHE SEQRES 16 A 279 VAL VAL GLY PHE ILE SER GLY SER ARG VAL SER MET LYS SEQRES 17 A 279 PRO GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU GLU SEQRES 18 A 279 ALA GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER PRO SEQRES 19 A 279 GLN GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE ILE SEQRES 20 A 279 VAL GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU GLU SEQRES 21 A 279 ALA ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA TYR SEQRES 22 A 279 LEU SER ARG LEU GLY VAL SEQRES 1 B 279 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 279 LEU VAL PRO ARG GLY SER HIS MET LYS GLU LEU SER PHE SEQRES 3 B 279 GLY ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL ALA SEQRES 4 B 279 SER LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR ASN SEQRES 5 B 279 LEU CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU LEU SEQRES 6 B 279 LEU GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS MET SEQRES 7 B 279 LEU LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR LEU SEQRES 8 B 279 ASP VAL MET LYS GLU LEU ILE THR LEU ALA LYS CSD HIS SEQRES 9 B 279 GLU PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP ILE SEQRES 10 B 279 GLY ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE PHE SEQRES 11 B 279 LYS ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS VAL SEQRES 12 B 279 VAL PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU VAL SEQRES 13 B 279 GLY LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA GLU SEQRES 14 B 279 MET SER SER THR GLY SER LEU ALA THR GLY ASP TYR THR SEQRES 15 B 279 ARG ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU PHE SEQRES 16 B 279 VAL VAL GLY PHE ILE SER GLY SER ARG VAL SER MET LYS SEQRES 17 B 279 PRO GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU GLU SEQRES 18 B 279 ALA GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER PRO SEQRES 19 B 279 GLN GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE ILE SEQRES 20 B 279 VAL GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU GLU SEQRES 21 B 279 ALA ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA TYR SEQRES 22 B 279 LEU SER ARG LEU GLY VAL MODRES 3MI2 CSD A 115 CYS 3-SULFINOALANINE MODRES 3MI2 CSD B 115 CYS 3-SULFINOALANINE HET CSD A 115 8 HET CSD B 115 8 HET PFU A 1 22 HET PFU B 1 22 HETNAM CSD 3-SULFINOALANINE HETNAM PFU (1S)-1,4-ANHYDRO-1-(5-CARBAMOYL-4-HYDROXY-1H-PYRAZOL-3- HETNAM 2 PFU YL)-5-O-PHOSPHONO-D-RIBITOL HETSYN CSD S-CYSTEINESULFINIC ACID; S-SULFINOCYSTEINE HETSYN PFU PYRAZOFURIN MONOPHOSPHATE FORMUL 1 CSD 2(C3 H7 N O4 S) FORMUL 3 PFU 2(C9 H14 N3 O9 P) FORMUL 5 HOH *692(H2 O) HELIX 1 1 SER A 37 ALA A 42 1 6 HELIX 2 2 HIS A 48 GLU A 62 1 15 HELIX 3 3 LEU A 73 GLY A 85 1 13 HELIX 4 4 PRO A 86 ILE A 88 5 3 HELIX 5 5 HIS A 94 LEU A 98 5 5 HELIX 6 6 THR A 102 GLU A 117 1 16 HELIX 7 7 ILE A 129 GLY A 139 1 11 HELIX 8 8 LYS A 143 ALA A 148 1 6 HELIX 9 9 SER A 159 LEU A 170 1 12 HELIX 10 10 GLY A 191 GLU A 203 1 13 HELIX 11 11 SER A 245 GLY A 251 1 7 HELIX 12 12 GLY A 261 SER A 266 1 6 HELIX 13 13 ASP A 269 GLY A 290 1 22 HELIX 14 14 SER B 37 ALA B 42 1 6 HELIX 15 15 HIS B 48 GLU B 62 1 15 HELIX 16 16 LEU B 73 GLY B 85 1 13 HELIX 17 17 PRO B 86 ILE B 88 5 3 HELIX 18 18 HIS B 94 LEU B 98 5 5 HELIX 19 19 THR B 102 GLU B 117 1 16 HELIX 20 20 ILE B 129 GLY B 139 1 11 HELIX 21 21 LYS B 143 ALA B 148 1 6 HELIX 22 22 SER B 159 LEU B 170 1 12 HELIX 23 23 GLY B 191 GLU B 203 1 13 HELIX 24 24 SER B 245 GLY B 251 1 7 HELIX 25 25 GLY B 261 SER B 266 1 6 HELIX 26 26 ASP B 269 GLY B 290 1 22 SHEET 1 A 9 LEU A 65 SER A 68 0 SHEET 2 A 9 MET A 90 THR A 93 1 O LYS A 92 N LEU A 67 SHEET 3 A 9 LEU A 119 PHE A 126 1 O ASP A 123 N THR A 93 SHEET 4 A 9 LEU A 150 HIS A 154 1 O HIS A 154 N PHE A 126 SHEET 5 A 9 GLY A 175 ILE A 179 1 O ILE A 179 N ALA A 153 SHEET 6 A 9 VAL A 208 ILE A 212 1 O VAL A 209 N CYS A 176 SHEET 7 A 9 LEU A 224 THR A 227 1 O LEU A 224 N PHE A 211 SHEET 8 A 9 ILE A 257 VAL A 260 1 O ILE A 257 N THR A 227 SHEET 9 A 9 LEU A 65 SER A 68 1 N CYS A 66 O ILE A 258 SHEET 1 B 2 GLY A 235 GLY A 236 0 SHEET 2 B 2 GLN A 242 TYR A 243 -1 O TYR A 243 N GLY A 235 SHEET 1 C 9 LEU B 65 SER B 68 0 SHEET 2 C 9 MET B 90 THR B 93 1 O LYS B 92 N LEU B 67 SHEET 3 C 9 LEU B 119 PHE B 126 1 O ASP B 123 N THR B 93 SHEET 4 C 9 LEU B 150 HIS B 154 1 O HIS B 154 N PHE B 126 SHEET 5 C 9 GLY B 175 ILE B 179 1 O ILE B 179 N ALA B 153 SHEET 6 C 9 VAL B 208 ILE B 212 1 O VAL B 209 N CYS B 176 SHEET 7 C 9 LEU B 224 THR B 227 1 O LEU B 226 N PHE B 211 SHEET 8 C 9 ILE B 257 VAL B 260 1 O ILE B 257 N THR B 227 SHEET 9 C 9 LEU B 65 SER B 68 1 N CYS B 66 O ILE B 258 SHEET 1 D 2 GLY B 235 GLY B 236 0 SHEET 2 D 2 GLN B 242 TYR B 243 -1 O TYR B 243 N GLY B 235 LINK C LYS A 114 N CSD A 115 1555 1555 1.33 LINK C CSD A 115 N HIS A 116 1555 1555 1.33 LINK C LYS B 114 N CSD B 115 1555 1555 1.33 LINK C CSD B 115 N HIS B 116 1555 1555 1.33 SITE 1 AC1 22 ASP A 128 ILE A 129 THR A 132 HOH B 4 SITE 2 AC1 22 HOH B 6 HOH B 10 SER B 68 ASP B 70 SITE 3 AC1 22 LYS B 92 HIS B 94 ASP B 123 LYS B 125 SITE 4 AC1 22 MET B 182 SER B 183 ILE B 212 PRO B 228 SITE 5 AC1 22 GLN B 241 TYR B 243 GLY B 261 ARG B 262 SITE 6 AC1 22 HOH B 299 HOH B 363 SITE 1 AC2 22 HOH A 9 HOH A 11 SER A 68 ASP A 70 SITE 2 AC2 22 LYS A 92 HIS A 94 ASP A 123 LYS A 125 SITE 3 AC2 22 MET A 182 SER A 183 ILE A 212 PRO A 228 SITE 4 AC2 22 GLN A 241 TYR A 243 GLY A 261 ARG A 262 SITE 5 AC2 22 HOH A 298 HOH A 304 HOH A 332 ASP B 128 SITE 6 AC2 22 ILE B 129 THR B 132 CRYST1 70.485 62.109 70.499 90.00 111.45 90.00 P 1 21 1 4 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 0.014187 0.000000 0.005573 0.00000 SCALE2 0.000000 0.016101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015240 0.00000