HEADER LYASE 26-NOV-07 3BGJ TITLE CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE TITLE 2 COVALENTLY MODIFIED BY 6-IODO-UMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE 5'-MONOPHOSPHATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: 5'-MONOPHOSPHATE SYNTHASE; COMPND 5 SYNONYM: UMP SYNTHASE, OMPDECASE, UMPS; 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, 6-IODO-UMP, DISEASE MUTATION, KEYWDS 3 GLYCOSYLTRANSFERASE, LYASE, MULTIFUNCTIONAL ENZYME, PYRIMIDINE KEYWDS 4 BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,H.L.TANG,A.M.BELLO,S.DEVALLA,L.P.KOTRA,E.F.PAI REVDAT 4 30-AUG-23 3BGJ 1 LINK REVDAT 3 13-JUL-11 3BGJ 1 VERSN REVDAT 2 24-FEB-09 3BGJ 1 VERSN REVDAT 1 18-NOV-08 3BGJ 0 JRNL AUTH Y.LIU,H.L.TANG,A.M.BELLO,S.DEVALLA,L.P.KOTRA,E.F.PAI JRNL TITL CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE JRNL TITL 2 DECARBOXYLASE COVALENTLY MODIFIED BY 6-IODO-UMP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 35629 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1877 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2552 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.2440 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 : 48 REMARK 3 SOLVENT ATOMS : 230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.02000 REMARK 3 B22 (A**2) : -1.56000 REMARK 3 B33 (A**2) : 2.55000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.71000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.171 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.149 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.719 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4197 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5688 ; 1.542 ; 1.992 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 543 ; 5.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;35.824 ;23.846 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 746 ;14.114 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;16.448 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 650 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3109 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2059 ; 0.230 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2916 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 276 ; 0.159 ; 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): 50 ; 0.197 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.200 ; 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): 2726 ; 0.881 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4239 ; 1.350 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1665 ; 2.385 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1449 ; 3.797 ; 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 3BGJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045492. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-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 : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90020 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37145 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.25900 REMARK 200 R SYM FOR SHELL (I) : 0.25900 REMARK 200 FOR SHELL : 4.540 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 (%): 45.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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 30.91050 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: 5290 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 ASP A 1 REMARK 465 ALA A 2 REMARK 465 GLU A 3 REMARK 465 THR A 4 REMARK 465 VAL A 5 REMARK 465 GLY A 6 REMARK 465 ARG A 7 REMARK 465 VAL A 8 REMARK 465 LYS A 9 REMARK 465 ARG A 10 REMARK 465 PHE A 11 REMARK 465 ILE A 12 REMARK 465 GLN A 13 REMARK 465 GLU A 14 REMARK 465 ASN A 15 REMARK 465 VAL A 16 REMARK 465 PHE A 17 REMARK 465 VAL A 18 REMARK 465 ALA A 19 REMARK 465 ALA A 20 REMARK 465 ASN A 21 REMARK 465 HIS A 22 REMARK 465 ASN A 23 REMARK 465 GLY A 24 REMARK 465 SER A 25 REMARK 465 PRO A 26 REMARK 465 LEU A 27 REMARK 465 SER A 28 REMARK 465 ILE A 29 REMARK 465 LYS A 30 REMARK 465 GLU A 31 REMARK 465 ALA A 32 REMARK 465 PRO A 33 REMARK 465 VAL A 291 REMARK 465 ASP B 1 REMARK 465 ALA B 2 REMARK 465 GLU B 3 REMARK 465 THR B 4 REMARK 465 VAL B 5 REMARK 465 GLY B 6 REMARK 465 ARG B 7 REMARK 465 VAL B 8 REMARK 465 LYS B 9 REMARK 465 ARG B 10 REMARK 465 PHE B 11 REMARK 465 ILE B 12 REMARK 465 GLN B 13 REMARK 465 GLU B 14 REMARK 465 ASN B 15 REMARK 465 VAL B 16 REMARK 465 PHE B 17 REMARK 465 VAL B 18 REMARK 465 ALA B 19 REMARK 465 ALA B 20 REMARK 465 ASN B 21 REMARK 465 HIS B 22 REMARK 465 ASN B 23 REMARK 465 GLY B 24 REMARK 465 SER B 25 REMARK 465 PRO B 26 REMARK 465 LEU B 27 REMARK 465 SER B 28 REMARK 465 ILE B 29 REMARK 465 LYS B 30 REMARK 465 GLU B 31 REMARK 465 ALA B 32 REMARK 465 PRO 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 ASP A 96 3.37 -69.65 REMARK 500 GLU A 117 72.52 68.00 REMARK 500 ALA A 127 60.38 -155.58 REMARK 500 TRP A 147 -12.87 -142.66 REMARK 500 ASP A 237 -169.08 -109.74 REMARK 500 GLU B 117 72.58 68.14 REMARK 500 ALA B 127 65.37 -158.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THERE IS A COVALENT BOND FORMED BETWEEN CARBON-6 REMARK 600 OF THE URIDINE RING OF UMP AND THE NZ-NITROGEN OF REMARK 600 LYS125 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P A3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U5P B3000 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B1000 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 STRUTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COMPLEXED WITH BMP REMARK 900 RELATED ID: 3BK0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 COMPLEXED WITH 5-CN-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 3BGJ A 1 291 UNP P11172 PYR5_HUMAN 190 480 DBREF 3BGJ B 1 291 UNP P11172 PYR5_HUMAN 190 480 SEQRES 1 A 291 ASP ALA GLU THR VAL GLY ARG VAL LYS ARG PHE ILE GLN SEQRES 2 A 291 GLU ASN VAL PHE VAL ALA ALA ASN HIS ASN GLY SER PRO SEQRES 3 A 291 LEU SER ILE LYS GLU ALA PRO LYS GLU LEU SER PHE GLY SEQRES 4 A 291 ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL ALA SER SEQRES 5 A 291 LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR ASN LEU SEQRES 6 A 291 CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU LEU LEU SEQRES 7 A 291 GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS MET LEU SEQRES 8 A 291 LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR LEU ASP SEQRES 9 A 291 VAL MET LYS GLU LEU ILE THR LEU ALA LYS CYS HIS GLU SEQRES 10 A 291 PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP ILE GLY SEQRES 11 A 291 ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE PHE LYS SEQRES 12 A 291 ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS VAL VAL SEQRES 13 A 291 PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU VAL GLY SEQRES 14 A 291 LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA GLU MET SEQRES 15 A 291 SER SER THR GLY SER LEU ALA THR GLY ASP TYR THR ARG SEQRES 16 A 291 ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU PHE VAL SEQRES 17 A 291 VAL GLY PHE ILE SER GLY SER ARG VAL SER MET LYS PRO SEQRES 18 A 291 GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU GLU ALA SEQRES 19 A 291 GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER PRO GLN SEQRES 20 A 291 GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE ILE VAL SEQRES 21 A 291 GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU GLU ALA SEQRES 22 A 291 ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA TYR LEU SEQRES 23 A 291 SER ARG LEU GLY VAL SEQRES 1 B 291 ASP ALA GLU THR VAL GLY ARG VAL LYS ARG PHE ILE GLN SEQRES 2 B 291 GLU ASN VAL PHE VAL ALA ALA ASN HIS ASN GLY SER PRO SEQRES 3 B 291 LEU SER ILE LYS GLU ALA PRO LYS GLU LEU SER PHE GLY SEQRES 4 B 291 ALA ARG ALA GLU LEU PRO ARG ILE HIS PRO VAL ALA SER SEQRES 5 B 291 LYS LEU LEU ARG LEU MET GLN LYS LYS GLU THR ASN LEU SEQRES 6 B 291 CYS LEU SER ALA ASP VAL SER LEU ALA ARG GLU LEU LEU SEQRES 7 B 291 GLN LEU ALA ASP ALA LEU GLY PRO SER ILE CYS MET LEU SEQRES 8 B 291 LYS THR HIS VAL ASP ILE LEU ASN ASP PHE THR LEU ASP SEQRES 9 B 291 VAL MET LYS GLU LEU ILE THR LEU ALA LYS CYS HIS GLU SEQRES 10 B 291 PHE LEU ILE PHE GLU ASP ARG LYS PHE ALA ASP ILE GLY SEQRES 11 B 291 ASN THR VAL LYS LYS GLN TYR GLU GLY GLY ILE PHE LYS SEQRES 12 B 291 ILE ALA SER TRP ALA ASP LEU VAL ASN ALA HIS VAL VAL SEQRES 13 B 291 PRO GLY SER GLY VAL VAL LYS GLY LEU GLN GLU VAL GLY SEQRES 14 B 291 LEU PRO LEU HIS ARG GLY CYS LEU LEU ILE ALA GLU MET SEQRES 15 B 291 SER SER THR GLY SER LEU ALA THR GLY ASP TYR THR ARG SEQRES 16 B 291 ALA ALA VAL ARG MET ALA GLU GLU HIS SER GLU PHE VAL SEQRES 17 B 291 VAL GLY PHE ILE SER GLY SER ARG VAL SER MET LYS PRO SEQRES 18 B 291 GLU PHE LEU HIS LEU THR PRO GLY VAL GLN LEU GLU ALA SEQRES 19 B 291 GLY GLY ASP ASN LEU GLY GLN GLN TYR ASN SER PRO GLN SEQRES 20 B 291 GLU VAL ILE GLY LYS ARG GLY SER ASP ILE ILE ILE VAL SEQRES 21 B 291 GLY ARG GLY ILE ILE SER ALA ALA ASP ARG LEU GLU ALA SEQRES 22 B 291 ALA GLU MET TYR ARG LYS ALA ALA TRP GLU ALA TYR LEU SEQRES 23 B 291 SER ARG LEU GLY VAL HET U5P A3000 21 HET U5P B3000 21 HET GOL B1000 6 HETNAM U5P URIDINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 U5P 2(C9 H13 N2 O9 P) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *230(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 HIS A 204 1 14 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 GLY B 191 HIS B 204 1 14 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 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 259 N THR A 227 SHEET 9 A 9 LEU A 65 SER A 68 1 N SER A 68 O VAL A 260 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 LEU B 119 N LEU B 91 SHEET 4 C 9 LEU B 150 HIS B 154 1 O LEU B 150 N GLU B 122 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 LINK NZ LYS A 125 C6 U5P A3000 1555 1555 1.30 LINK NZ LYS B 125 C6 U5P B3000 1555 1555 1.32 SITE 1 AC1 18 SER A 68 ASP A 70 LYS A 92 HIS A 94 SITE 2 AC1 18 ASP A 123 LYS A 125 MET A 182 SER A 183 SITE 3 AC1 18 PRO A 228 GLN A 241 TYR A 243 GLY A 261 SITE 4 AC1 18 ARG A 262 HOH A3002 HOH A3005 HOH A3026 SITE 5 AC1 18 ASP B 128 THR B 132 SITE 1 AC2 18 ASP A 128 THR A 132 SER B 68 ASP B 70 SITE 2 AC2 18 LYS B 92 HIS B 94 ASP B 123 LYS B 125 SITE 3 AC2 18 MET B 182 SER B 183 PRO B 228 GLN B 241 SITE 4 AC2 18 TYR B 243 GLY B 261 ARG B 262 HOH B3001 SITE 5 AC2 18 HOH B3002 HOH B3006 SITE 1 AC3 3 LEU B 232 GLU B 233 ALA B 234 CRYST1 69.803 61.821 70.881 90.00 111.66 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 0.014326 0.000000 0.005690 0.00000 SCALE2 0.000000 0.016176 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015180 0.00000