HEADER LYASE 16-OCT-08 3EWW TITLE D312N MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN TITLE 2 COMPLEX WITH 6-CYANO-UMP, COVALENT ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE-5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 224-480; COMPND 5 SYNONYM: OMPDECASE; COMPND 6 EC: 4.1.1.23; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: UMPS; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETM-30 KEYWDS DECARBOXYLASE, TIM BARREL, UNUSUAL CATALYSIS, DISEASE MUTATION, KEYWDS 2 GLYCOSYLTRANSFERASE, LYASE, MULTIFUNCTIONAL ENZYME, PYRIMIDINE KEYWDS 3 BIOSYNTHESIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR D.HEINRICH,J.WITTMANN,U.DIEDERICHSEN,M.RUDOLPH REVDAT 7 06-NOV-24 3EWW 1 REMARK REVDAT 6 27-DEC-23 3EWW 1 REMARK REVDAT 5 20-OCT-21 3EWW 1 REMARK SEQADV LINK REVDAT 4 25-OCT-17 3EWW 1 REMARK REVDAT 3 13-JUL-11 3EWW 1 VERSN REVDAT 2 15-DEC-09 3EWW 1 JRNL REVDAT 1 07-APR-09 3EWW 0 JRNL AUTH D.HEINRICH,U.DIEDERICHSEN,M.G.RUDOLPH JRNL TITL LYS314 IS A NUCLEOPHILE IN NON-CLASSICAL REACTIONS OF JRNL TITL 2 OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE JRNL REF CHEMISTRY V. 15 6619 2009 JRNL REFN ISSN 0947-6539 JRNL PMID 19472232 JRNL DOI 10.1002/CHEM.200900397 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 208905 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10994 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) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 15115 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.3710 REMARK 3 BIN FREE R VALUE SET COUNT : 801 REMARK 3 BIN FREE R VALUE : 0.3600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3932 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 52 REMARK 3 SOLVENT ATOMS : 546 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : -0.46000 REMARK 3 B33 (A**2) : 0.81000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.84000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.031 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.027 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.307 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4295 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2944 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5854 ; 1.670 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7251 ; 2.025 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 587 ; 5.819 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;36.607 ;23.864 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 807 ;12.573 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;13.953 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 678 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4792 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 839 ; 0.003 ; 0.020 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): 2663 ; 1.600 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1100 ; 0.689 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4304 ; 2.309 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1632 ; 3.320 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1513 ; 4.869 ; 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): 7239 ; 1.499 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 546 ; 6.714 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7135 ; 2.992 ; 3.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3EWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049868. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 220824 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 42.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.81500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: COMO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH 8.0, 1.8 M REMARK 280 (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 300.0K 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 30.73950 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: 3820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.4 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 GLY A 221 REMARK 465 ALA A 222 REMARK 465 VAL A 480 REMARK 465 GLY B 221 REMARK 465 ALA B 222 REMARK 465 VAL B 480 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS B 314 N8 U1P B 481 2.09 REMARK 500 NZ LYS B 332 O HOH B 563 2.10 REMARK 500 O HOH A 707 O HOH A 709 2.11 REMARK 500 CE LYS B 314 C7 U1P B 481 2.17 REMARK 500 NZ LYS A 314 N8 U1P A 482 2.19 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 259 50.79 -92.61 REMARK 500 GLU A 306 75.94 65.73 REMARK 500 ALA A 316 53.93 -162.35 REMARK 500 TRP A 336 -17.19 -142.98 REMARK 500 ASP B 259 54.93 -92.95 REMARK 500 GLU B 306 77.33 68.49 REMARK 500 ALA B 316 52.61 -163.18 REMARK 500 PHE B 396 -39.91 -137.00 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 GOL A 481 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U1P A 482 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE U1P B 481 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EWU RELATED DB: PDB REMARK 900 D312N MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN REMARK 900 COMPLEX WITH 6-ACETYL-UMP, COVALENT ADDUCT REMARK 900 RELATED ID: 3EWX RELATED DB: PDB REMARK 900 K314A MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN REMARK 900 COMPLEX WITH 6-AZIDO-UMP, DEGRADED TO BMP REMARK 900 RELATED ID: 3EWY RELATED DB: PDB REMARK 900 K314A MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE REMARK 900 SOAKED WITH OMP, DECARBOXYLATED TO UMP REMARK 900 RELATED ID: 3EWZ RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH 5- REMARK 900 CYANO-UMP REMARK 900 RELATED ID: 3EX0 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH 6- REMARK 900 ACETYL-UMP REMARK 900 RELATED ID: 3EX1 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE SOAKED WITH 6-CYANO- REMARK 900 UMP, CONVERTED TO UMP REMARK 900 RELATED ID: 3EX2 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH 6- REMARK 900 CYANO-UMP REMARK 900 RELATED ID: 3EX3 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH 6- REMARK 900 AZIDO-UMP, COVALENT ADDUCT REMARK 900 RELATED ID: 3EX4 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH BMP REMARK 900 RELATED ID: 3EX5 RELATED DB: PDB REMARK 900 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH 6- REMARK 900 MERCAPTO-UMP REMARK 900 RELATED ID: 3EX6 RELATED DB: PDB REMARK 900 D312N MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN REMARK 900 COMPLEX WITH 6-AZIDO-UMP, COVALENT ADDUCT DBREF 3EWW A 224 480 UNP P11172 PYR5_HUMAN 224 480 DBREF 3EWW B 224 480 UNP P11172 PYR5_HUMAN 224 480 SEQADV 3EWW GLY A 221 UNP P11172 EXPRESSION TAG SEQADV 3EWW ALA A 222 UNP P11172 EXPRESSION TAG SEQADV 3EWW MET A 223 UNP P11172 EXPRESSION TAG SEQADV 3EWW ASN A 312 UNP P11172 ASP 312 ENGINEERED MUTATION SEQADV 3EWW GLY B 221 UNP P11172 EXPRESSION TAG SEQADV 3EWW ALA B 222 UNP P11172 EXPRESSION TAG SEQADV 3EWW MET B 223 UNP P11172 EXPRESSION TAG SEQADV 3EWW ASN B 312 UNP P11172 ASP 312 ENGINEERED MUTATION SEQRES 1 A 260 GLY ALA MET GLU LEU SER PHE GLY ALA ARG ALA GLU LEU SEQRES 2 A 260 PRO ARG ILE HIS PRO VAL ALA SER LYS LEU LEU ARG LEU SEQRES 3 A 260 MET GLN LYS LYS GLU THR ASN LEU CYS LEU SER ALA ASP SEQRES 4 A 260 VAL SER LEU ALA ARG GLU LEU LEU GLN LEU ALA ASP ALA SEQRES 5 A 260 LEU GLY PRO SER ILE CYS MET LEU LYS THR HIS VAL ASP SEQRES 6 A 260 ILE LEU ASN ASP PHE THR LEU ASP VAL MET LYS GLU LEU SEQRES 7 A 260 ILE THR LEU ALA LYS CYS HIS GLU PHE LEU ILE PHE GLU SEQRES 8 A 260 ASN ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LYS SEQRES 9 A 260 GLN TYR GLU GLY GLY ILE PHE LYS ILE ALA SER TRP ALA SEQRES 10 A 260 ASP LEU VAL ASN ALA HIS VAL VAL PRO GLY SER GLY VAL SEQRES 11 A 260 VAL LYS GLY LEU GLN GLU VAL GLY LEU PRO LEU HIS ARG SEQRES 12 A 260 GLY CYS LEU LEU ILE ALA GLU MET SER SER THR GLY SER SEQRES 13 A 260 LEU ALA THR GLY ASP TYR THR ARG ALA ALA VAL ARG MET SEQRES 14 A 260 ALA GLU GLU HIS SER GLU PHE VAL VAL GLY PHE ILE SER SEQRES 15 A 260 GLY SER ARG VAL SER MET LYS PRO GLU PHE LEU HIS LEU SEQRES 16 A 260 THR PRO GLY VAL GLN LEU GLU ALA GLY GLY ASP ASN LEU SEQRES 17 A 260 GLY GLN GLN TYR ASN SER PRO GLN GLU VAL ILE GLY LYS SEQRES 18 A 260 ARG GLY SER ASP ILE ILE ILE VAL GLY ARG GLY ILE ILE SEQRES 19 A 260 SER ALA ALA ASP ARG LEU GLU ALA ALA GLU MET TYR ARG SEQRES 20 A 260 LYS ALA ALA TRP GLU ALA TYR LEU SER ARG LEU GLY VAL SEQRES 1 B 260 GLY ALA MET GLU LEU SER PHE GLY ALA ARG ALA GLU LEU SEQRES 2 B 260 PRO ARG ILE HIS PRO VAL ALA SER LYS LEU LEU ARG LEU SEQRES 3 B 260 MET GLN LYS LYS GLU THR ASN LEU CYS LEU SER ALA ASP SEQRES 4 B 260 VAL SER LEU ALA ARG GLU LEU LEU GLN LEU ALA ASP ALA SEQRES 5 B 260 LEU GLY PRO SER ILE CYS MET LEU LYS THR HIS VAL ASP SEQRES 6 B 260 ILE LEU ASN ASP PHE THR LEU ASP VAL MET LYS GLU LEU SEQRES 7 B 260 ILE THR LEU ALA LYS CYS HIS GLU PHE LEU ILE PHE GLU SEQRES 8 B 260 ASN ARG LYS PHE ALA ASP ILE GLY ASN THR VAL LYS LYS SEQRES 9 B 260 GLN TYR GLU GLY GLY ILE PHE LYS ILE ALA SER TRP ALA SEQRES 10 B 260 ASP LEU VAL ASN ALA HIS VAL VAL PRO GLY SER GLY VAL SEQRES 11 B 260 VAL LYS GLY LEU GLN GLU VAL GLY LEU PRO LEU HIS ARG SEQRES 12 B 260 GLY CYS LEU LEU ILE ALA GLU MET SER SER THR GLY SER SEQRES 13 B 260 LEU ALA THR GLY ASP TYR THR ARG ALA ALA VAL ARG MET SEQRES 14 B 260 ALA GLU GLU HIS SER GLU PHE VAL VAL GLY PHE ILE SER SEQRES 15 B 260 GLY SER ARG VAL SER MET LYS PRO GLU PHE LEU HIS LEU SEQRES 16 B 260 THR PRO GLY VAL GLN LEU GLU ALA GLY GLY ASP ASN LEU SEQRES 17 B 260 GLY GLN GLN TYR ASN SER PRO GLN GLU VAL ILE GLY LYS SEQRES 18 B 260 ARG GLY SER ASP ILE ILE ILE VAL GLY ARG GLY ILE ILE SEQRES 19 B 260 SER ALA ALA ASP ARG LEU GLU ALA ALA GLU MET TYR ARG SEQRES 20 B 260 LYS ALA ALA TRP GLU ALA TYR LEU SER ARG LEU GLY VAL HET GOL A 481 6 HET U1P A 482 23 HET U1P B 481 23 HETNAM GOL GLYCEROL HETNAM U1P 6-[(E)-IMINOMETHYL]URIDINE 5'-PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 U1P 2(C10 H14 N3 O9 P) FORMUL 6 HOH *546(H2 O) HELIX 1 1 SER A 226 ALA A 231 1 6 HELIX 2 2 HIS A 237 GLU A 251 1 15 HELIX 3 3 LEU A 262 GLY A 274 1 13 HELIX 4 4 PRO A 275 ILE A 277 5 3 HELIX 5 5 HIS A 283 LEU A 287 5 5 HELIX 6 6 THR A 291 GLU A 306 1 16 HELIX 7 7 ILE A 318 GLY A 328 1 11 HELIX 8 8 LYS A 332 TRP A 336 5 5 HELIX 9 9 SER A 348 LEU A 359 1 12 HELIX 10 10 GLY A 380 HIS A 393 1 14 HELIX 11 11 SER A 434 GLY A 440 1 7 HELIX 12 12 GLY A 450 SER A 455 1 6 HELIX 13 13 ASP A 458 GLY A 479 1 22 HELIX 14 14 SER B 226 ALA B 231 1 6 HELIX 15 15 HIS B 237 GLU B 251 1 15 HELIX 16 16 LEU B 262 GLY B 274 1 13 HELIX 17 17 PRO B 275 ILE B 277 5 3 HELIX 18 18 HIS B 283 LEU B 287 5 5 HELIX 19 19 THR B 291 GLU B 306 1 16 HELIX 20 20 ILE B 318 GLY B 328 1 11 HELIX 21 21 LYS B 332 TRP B 336 5 5 HELIX 22 22 SER B 348 LEU B 359 1 12 HELIX 23 23 GLY B 380 HIS B 393 1 14 HELIX 24 24 SER B 434 LYS B 441 1 8 HELIX 25 25 GLY B 450 SER B 455 1 6 HELIX 26 26 ASP B 458 GLY B 479 1 22 SHEET 1 A 9 LEU A 254 SER A 257 0 SHEET 2 A 9 MET A 279 THR A 282 1 O LYS A 281 N LEU A 256 SHEET 3 A 9 LEU A 308 PHE A 315 1 O ASN A 312 N THR A 282 SHEET 4 A 9 LEU A 339 HIS A 343 1 O HIS A 343 N PHE A 315 SHEET 5 A 9 GLY A 364 ILE A 368 1 O LEU A 366 N VAL A 340 SHEET 6 A 9 VAL A 397 ILE A 401 1 O VAL A 398 N CYS A 365 SHEET 7 A 9 LEU A 413 THR A 416 1 O LEU A 413 N PHE A 400 SHEET 8 A 9 ILE A 446 VAL A 449 1 O ILE A 446 N THR A 416 SHEET 9 A 9 LEU A 254 SER A 257 1 N CYS A 255 O ILE A 447 SHEET 1 B 2 GLY A 424 GLY A 425 0 SHEET 2 B 2 GLN A 431 TYR A 432 -1 O TYR A 432 N GLY A 424 SHEET 1 C 9 LEU B 254 SER B 257 0 SHEET 2 C 9 MET B 279 THR B 282 1 O LYS B 281 N LEU B 256 SHEET 3 C 9 LEU B 308 PHE B 315 1 O PHE B 310 N LEU B 280 SHEET 4 C 9 LEU B 339 HIS B 343 1 O HIS B 343 N PHE B 315 SHEET 5 C 9 GLY B 364 ILE B 368 1 O ILE B 368 N ALA B 342 SHEET 6 C 9 VAL B 397 ILE B 401 1 O VAL B 398 N CYS B 365 SHEET 7 C 9 LEU B 413 THR B 416 1 O LEU B 415 N PHE B 400 SHEET 8 C 9 ILE B 446 VAL B 449 1 O ILE B 446 N THR B 416 SHEET 9 C 9 LEU B 254 SER B 257 1 N CYS B 255 O ILE B 447 SHEET 1 D 2 GLY B 424 GLY B 425 0 SHEET 2 D 2 GLN B 431 TYR B 432 -1 O TYR B 432 N GLY B 424 LINK NZ LYS A 314 C7 U1P A 482 1555 1555 1.27 LINK NZ LYS B 314 C7 U1P B 481 1555 1555 1.24 SITE 1 AC1 8 LYS A 242 ALA A 302 LYS A 303 PHE A 307 SITE 2 AC1 8 LEU A 308 ASP A 338 HOH A 565 HOH A 699 SITE 1 AC2 19 SER A 257 LYS A 281 HIS A 283 ASN A 312 SITE 2 AC2 19 LYS A 314 ASN A 341 MET A 371 SER A 372 SITE 3 AC2 19 PRO A 417 GLN A 430 TYR A 432 GLY A 450 SITE 4 AC2 19 ARG A 451 HOH A 483 HOH A 486 HOH A 525 SITE 5 AC2 19 ASP B 317 ILE B 318 THR B 321 SITE 1 AC3 19 ASP A 317 ILE A 318 THR A 321 LYS B 281 SITE 2 AC3 19 HIS B 283 ASN B 312 LYS B 314 ASN B 341 SITE 3 AC3 19 MET B 371 SER B 372 PRO B 417 GLN B 430 SITE 4 AC3 19 TYR B 432 GLY B 450 ARG B 451 HOH B 483 SITE 5 AC3 19 HOH B 486 HOH B 572 HOH B 609 CRYST1 69.527 61.479 70.491 90.00 113.13 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 0.014383 0.000000 0.006144 0.00000 SCALE2 0.000000 0.016266 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015426 0.00000