HEADER LYASE 05-DEC-07 3BK0 TITLE CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE TITLE 2 COMPLEXED WITH 5-CN-UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: UMP SYNTHASE, OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, COMPND 5 OMPDECASE; COMPND 6 EC: 4.1.1.23; COMPND 7 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: UMPS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS UMP SYNTHASE, C-TERMINAL DOMAIN, OROTIDINE 5'-MONOPHOSPHATE KEYWDS 2 DECARBOXYLASE, HUMAN, 5-CN-UMP, DISEASE MUTATION, KEYWDS 3 GLYCOSYLTRANSFERASE, LYASE, MULTIFUNCTIONAL ENZYME, PYRIMIDINE KEYWDS 4 BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,H.L.TANG,M.E.M.AVINA,L.P.KOTRA,E.F.PAI REVDAT 4 30-AUG-23 3BK0 1 REMARK SEQADV REVDAT 3 13-JUL-11 3BK0 1 VERSN REVDAT 2 24-FEB-09 3BK0 1 VERSN REVDAT 1 18-NOV-08 3BK0 0 JRNL AUTH Y.LIU,H.L.TANG,M.E.M.AVINA,L.P.KOTRA,E.F.PAI JRNL TITL CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE JRNL TITL 2 DECARBOXYLASE COMPLEXED WITH 5-CN-UMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 78.3 REMARK 3 NUMBER OF REFLECTIONS : 55585 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2938 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.63 REMARK 3 REFLECTION IN BIN (WORKING SET) : 969 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 18.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 49 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3934 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : 2.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.785 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4325 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5880 ; 1.514 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 571 ; 6.039 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;36.328 ;23.873 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 780 ;12.790 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.749 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3236 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2191 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3093 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 325 ; 0.134 ; 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): 44 ; 0.250 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.168 ; 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): 2810 ; 0.969 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4385 ; 1.486 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1701 ; 2.475 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1495 ; 3.951 ; 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 3BK0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045614. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-AUG-07 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) : 0.97934 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 : 58523 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 78.5 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 14.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 21.7 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : 0.32300 REMARK 200 FOR SHELL : 1.950 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 (%): 46.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 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 30.77700 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: 4600 ANGSTROM**2 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 ALA A 69 71.64 -103.02 REMARK 500 GLU A 117 73.80 68.37 REMARK 500 ALA A 127 42.42 -158.53 REMARK 500 TRP A 147 -16.25 -151.53 REMARK 500 PHE A 207 -36.83 -130.24 REMARK 500 GLU B 117 73.75 64.40 REMARK 500 ALA B 127 45.33 -157.68 REMARK 500 PHE B 207 -36.54 -131.65 REMARK 500 ASP B 237 -166.18 -111.03 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 SO4 A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNU A 1000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CNU B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 2001 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 COMPLEXED 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: 3BVJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COMPLEXED WITH XMP DBREF 3BK0 A 34 291 UNP P11172 PYR5_HUMAN 223 480 DBREF 3BK0 B 34 291 UNP P11172 PYR5_HUMAN 223 480 SEQADV 3BK0 MET A 13 UNP P11172 EXPRESSION TAG SEQADV 3BK0 GLY A 14 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER A 15 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER A 16 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 17 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 18 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 19 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 20 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 21 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 22 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER A 23 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER A 24 UNP P11172 EXPRESSION TAG SEQADV 3BK0 GLY A 25 UNP P11172 EXPRESSION TAG SEQADV 3BK0 LEU A 26 UNP P11172 EXPRESSION TAG SEQADV 3BK0 VAL A 27 UNP P11172 EXPRESSION TAG SEQADV 3BK0 PRO A 28 UNP P11172 EXPRESSION TAG SEQADV 3BK0 ARG A 29 UNP P11172 EXPRESSION TAG SEQADV 3BK0 GLY A 30 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER A 31 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS A 32 UNP P11172 EXPRESSION TAG SEQADV 3BK0 MET A 33 UNP P11172 EXPRESSION TAG SEQADV 3BK0 MET B 13 UNP P11172 EXPRESSION TAG SEQADV 3BK0 GLY B 14 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER B 15 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER B 16 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 17 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 18 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 19 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 20 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 21 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 22 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER B 23 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER B 24 UNP P11172 EXPRESSION TAG SEQADV 3BK0 GLY B 25 UNP P11172 EXPRESSION TAG SEQADV 3BK0 LEU B 26 UNP P11172 EXPRESSION TAG SEQADV 3BK0 VAL B 27 UNP P11172 EXPRESSION TAG SEQADV 3BK0 PRO B 28 UNP P11172 EXPRESSION TAG SEQADV 3BK0 ARG B 29 UNP P11172 EXPRESSION TAG SEQADV 3BK0 GLY B 30 UNP P11172 EXPRESSION TAG SEQADV 3BK0 SER B 31 UNP P11172 EXPRESSION TAG SEQADV 3BK0 HIS B 32 UNP P11172 EXPRESSION TAG SEQADV 3BK0 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 CYS 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 CYS 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 HET SO4 A3000 5 HET SO4 A3001 5 HET CNU A1000 23 HET GOL A2000 6 HET GOL A2001 6 HET CNU B1001 23 HETNAM SO4 SULFATE ION HETNAM CNU 5-CYANO-URIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN CNU 5-CYANO-UMP; 5-CYANOURIDINE 5'-(DIHYDROGEN PHOSPHATE) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 CNU 2(C10 H12 N3 O9 P) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 9 HOH *256(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 TRP A 147 5 5 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 LYS A 252 1 8 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 TRP B 147 5 5 HELIX 22 22 SER B 159 LEU B 170 1 12 HELIX 23 23 THR B 190 HIS B 204 1 15 HELIX 24 24 SER B 245 LYS B 252 1 8 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 PHE A 121 N LEU A 91 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 LEU A 177 N VAL A 151 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 259 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 PHE B 121 N LEU B 91 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 224 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 SITE 1 AC1 2 GLY A 39 GLU A 43 SITE 1 AC2 19 SER A 68 ASP A 70 LYS A 92 HIS A 94 SITE 2 AC2 19 ASP A 123 ILE A 179 MET A 182 SER A 183 SITE 3 AC2 19 ILE A 212 PRO A 228 GLN A 241 TYR A 243 SITE 4 AC2 19 GLY A 261 ARG A 262 HOH A3002 HOH A3006 SITE 5 AC2 19 HOH A3074 ASP B 128 THR B 132 SITE 1 AC3 20 ASP A 128 ILE A 129 THR A 132 SER B 68 SITE 2 AC3 20 ASP B 70 LYS B 92 HIS B 94 ASP B 123 SITE 3 AC3 20 ILE B 179 MET B 182 SER B 183 ILE B 212 SITE 4 AC3 20 PRO B 228 GLN B 241 TYR B 243 GLY B 261 SITE 5 AC3 20 ARG B 262 HOH B1002 HOH B1005 HOH B1015 SITE 1 AC4 6 LYS A 53 ALA A 113 GLU A 117 PHE A 118 SITE 2 AC4 6 ASP A 149 HOH A3099 SITE 1 AC5 5 ARG A 46 HIS A 48 PRO A 49 SER A 205 SITE 2 AC5 5 HOH A3117 CRYST1 69.552 61.554 70.989 90.00 111.81 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 0.014378 0.000000 0.005752 0.00000 SCALE2 0.000000 0.016246 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015172 0.00000