HEADER TRANSCRIPTION 19-NOV-04 1Y1T TITLE CRYSTAL STRUCTURE OF THE URIDINE PHOSPHORYLASE FROM SALMONELLA TITLE 2 TYPHIMURIUM AT 1.77A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: URIDINE PHOSPHORYLASE; COMPND 3 CHAIN: A, F; COMPND 4 SYNONYM: URDPASE, UPASE; COMPND 5 EC: 2.4.2.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA TYPHIMURIUM LT2; SOURCE 3 ORGANISM_TAXID: 99287; SOURCE 4 STRAIN: LT2; SOURCE 5 GENE: UDP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PBLUESCRIPT IISK KEYWDS NUCLEOSIDE PHOSPHORYLASE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.G.GABDOULKHAKOV,M.V.DONTSOVA,G.S.KACHALOVA,C.BETZEL,S.E.EALICK, AUTHOR 2 A.M.MIKHAILOV REVDAT 5 23-AUG-23 1Y1T 1 REMARK REVDAT 4 11-OCT-17 1Y1T 1 REMARK REVDAT 3 13-JUL-11 1Y1T 1 VERSN REVDAT 2 24-FEB-09 1Y1T 1 VERSN REVDAT 1 22-NOV-05 1Y1T 0 JRNL AUTH A.G.GABDOULKHAKOV,M.V.DONTSOVA,G.S.KACHALOVA,C.BETZEL, JRNL AUTH 2 S.E.EALICK,A.M.MIKHAILOV JRNL TITL CRYSTAL STRUCTURES OF SALMONELLA TYPHIMURIUM URIDINE JRNL TITL 2 PHOSPHORYLASE IN NATIVE AND THREE COMPLEXES FORMS - WITH JRNL TITL 3 URIDINE, URACIL AND SULFATE. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 4637088.680 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 38496 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) : 0.184 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1925 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6151 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 323 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3483 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 279 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.42000 REMARK 3 B22 (A**2) : -3.42000 REMARK 3 B33 (A**2) : 6.85000 REMARK 3 B12 (A**2) : -1.03000 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) : 0.19 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 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) : 2.710 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.770 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.340 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.120 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 64.03 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 : GOL.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : GOL.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1Y1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000031008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8126 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38496 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 25.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 1.770 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.64 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.460 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP V. 7.3 REMARK 200 STARTING MODEL: PDB ENTRY 1SJ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, SODIUM-ACETATE TRIHYDRATE, REMARK 280 PH 5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 75.41000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.53798 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.94667 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 75.41000 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 43.53798 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.94667 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 75.41000 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 43.53798 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.94667 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 87.07597 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 31.89333 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 87.07597 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 31.89333 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 87.07597 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 31.89333 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 17260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -168.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, F 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 BIOMT1 2 -0.500000 -0.866025 0.000000 150.82000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 75.41000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 130.61395 REMARK 350 BIOMT3 3 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 1001 REMARK 465 SER A 1002 REMARK 465 LYS A 1003 REMARK 465 MET F 2001 REMARK 465 SER F 2002 REMARK 465 LYS F 2003 REMARK 465 TYR F 2163 REMARK 465 PRO F 2164 REMARK 465 GLY F 2165 REMARK 465 GLN F 2166 REMARK 465 GLU F 2167 REMARK 465 ARG F 2168 REMARK 465 TYR F 2169 REMARK 465 ASP F 2170 REMARK 465 THR F 2171 REMARK 465 TYR F 2172 REMARK 465 SER F 2173 REMARK 465 GLY F 2174 REMARK 465 ARG F 2175 REMARK 465 VAL F 2176 REMARK 465 VAL F 2177 REMARK 465 ARG F 2178 REMARK 465 ARG F 2179 REMARK 465 PHE F 2180 REMARK 465 LYS F 2181 REMARK 465 GLY F 2182 REMARK 465 ARG F 2223 REMARK 465 THR F 2224 REMARK 465 GLN F 2225 REMARK 465 GLN F 2226 REMARK 465 GLU F 2227 REMARK 465 ILE F 2228 REMARK 465 PRO F 2229 REMARK 465 ASN F 2230 REMARK 465 ALA F 2231 REMARK 465 GLU F 2232 REMARK 465 THR F 2233 REMARK 465 MET F 2234 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 MET F2184 C GLU F2185 N 0.157 REMARK 500 REMARK 500 REMARK: NULL 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 MET F2184 O - C - N ANGL. DEV. = 10.2 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 ARG A1048 -137.31 59.88 REMARK 500 LEU A1116 38.39 -99.03 REMARK 500 TYR A1163 -81.89 -96.11 REMARK 500 ALA A1231 -32.31 -36.87 REMARK 500 GLU A1232 48.12 -93.69 REMARK 500 THR A1233 -18.72 -45.44 REMARK 500 MET A1234 -61.69 -131.21 REMARK 500 LYS A1235 -88.15 -16.19 REMARK 500 ARG F2048 -131.99 52.19 REMARK 500 MET F2184 -61.91 -178.30 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 F 4001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 5001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SJ9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE URIDINE PHOSPHORYLASE FROM SALMONELLA REMARK 900 TYPHIMURIUM AT 2.5A RESOLUTION REMARK 900 RELATED ID: 1RYZ RELATED DB: PDB REMARK 900 URIDINE PHOSPHORYLASE FROM SALMONELLA TYPHIMURIUM CRYSTAL STRUCTURE REMARK 900 AT 2.9 A RESOLUTION REMARK 900 RELATED ID: 1Y1Q RELATED DB: PDB REMARK 900 RELATED ID: 1Y1R RELATED DB: PDB REMARK 900 RELATED ID: 1Y1S RELATED DB: PDB DBREF 1Y1T A 1001 1253 UNP P0A1F6 UDP_SALTY 0 252 DBREF 1Y1T F 2001 2253 UNP P0A1F6 UDP_SALTY 0 252 SEQRES 1 A 253 MET SER LYS SER ASP VAL PHE HIS LEU GLY LEU THR LYS SEQRES 2 A 253 ASN ASP LEU GLN GLY ALA GLN LEU ALA ILE VAL PRO GLY SEQRES 3 A 253 ASP PRO GLU ARG VAL GLU LYS ILE ALA ALA LEU MET ASP SEQRES 4 A 253 LYS PRO VAL LYS LEU ALA SER HIS ARG GLU PHE THR SER SEQRES 5 A 253 TRP ARG ALA GLU LEU ASP GLY LYS ALA VAL ILE VAL CYS SEQRES 6 A 253 SER THR GLY ILE GLY GLY PRO SER THR SER ILE ALA VAL SEQRES 7 A 253 GLU GLU LEU ALA GLN LEU GLY ILE ARG THR PHE LEU ARG SEQRES 8 A 253 ILE GLY THR THR GLY ALA ILE GLN PRO HIS ILE ASN VAL SEQRES 9 A 253 GLY ASP VAL LEU VAL THR THR ALA SER VAL ARG LEU ASP SEQRES 10 A 253 GLY ALA SER LEU HIS PHE ALA PRO MET GLU PHE PRO ALA SEQRES 11 A 253 VAL ALA ASP PHE ALA CYS THR THR ALA LEU VAL GLU ALA SEQRES 12 A 253 ALA LYS SER ILE GLY ALA THR THR HIS VAL GLY VAL THR SEQRES 13 A 253 ALA SER SER ASP THR PHE TYR PRO GLY GLN GLU ARG TYR SEQRES 14 A 253 ASP THR TYR SER GLY ARG VAL VAL ARG ARG PHE LYS GLY SEQRES 15 A 253 SER MET GLU GLU TRP GLN ALA MET GLY VAL MET ASN TYR SEQRES 16 A 253 GLU MET GLU SER ALA THR LEU LEU THR MET CYS ALA SER SEQRES 17 A 253 GLN GLY LEU ARG ALA GLY MET VAL ALA GLY VAL ILE VAL SEQRES 18 A 253 ASN ARG THR GLN GLN GLU ILE PRO ASN ALA GLU THR MET SEQRES 19 A 253 LYS GLN THR GLU SER HIS ALA VAL LYS ILE VAL VAL GLU SEQRES 20 A 253 ALA ALA ARG ARG LEU LEU SEQRES 1 F 253 MET SER LYS SER ASP VAL PHE HIS LEU GLY LEU THR LYS SEQRES 2 F 253 ASN ASP LEU GLN GLY ALA GLN LEU ALA ILE VAL PRO GLY SEQRES 3 F 253 ASP PRO GLU ARG VAL GLU LYS ILE ALA ALA LEU MET ASP SEQRES 4 F 253 LYS PRO VAL LYS LEU ALA SER HIS ARG GLU PHE THR SER SEQRES 5 F 253 TRP ARG ALA GLU LEU ASP GLY LYS ALA VAL ILE VAL CYS SEQRES 6 F 253 SER THR GLY ILE GLY GLY PRO SER THR SER ILE ALA VAL SEQRES 7 F 253 GLU GLU LEU ALA GLN LEU GLY ILE ARG THR PHE LEU ARG SEQRES 8 F 253 ILE GLY THR THR GLY ALA ILE GLN PRO HIS ILE ASN VAL SEQRES 9 F 253 GLY ASP VAL LEU VAL THR THR ALA SER VAL ARG LEU ASP SEQRES 10 F 253 GLY ALA SER LEU HIS PHE ALA PRO MET GLU PHE PRO ALA SEQRES 11 F 253 VAL ALA ASP PHE ALA CYS THR THR ALA LEU VAL GLU ALA SEQRES 12 F 253 ALA LYS SER ILE GLY ALA THR THR HIS VAL GLY VAL THR SEQRES 13 F 253 ALA SER SER ASP THR PHE TYR PRO GLY GLN GLU ARG TYR SEQRES 14 F 253 ASP THR TYR SER GLY ARG VAL VAL ARG ARG PHE LYS GLY SEQRES 15 F 253 SER MET GLU GLU TRP GLN ALA MET GLY VAL MET ASN TYR SEQRES 16 F 253 GLU MET GLU SER ALA THR LEU LEU THR MET CYS ALA SER SEQRES 17 F 253 GLN GLY LEU ARG ALA GLY MET VAL ALA GLY VAL ILE VAL SEQRES 18 F 253 ASN ARG THR GLN GLN GLU ILE PRO ASN ALA GLU THR MET SEQRES 19 F 253 LYS GLN THR GLU SER HIS ALA VAL LYS ILE VAL VAL GLU SEQRES 20 F 253 ALA ALA ARG ARG LEU LEU HET GOL A5001 6 HET SO4 F4001 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *279(H2 O) HELIX 1 1 THR A 1012 GLN A 1017 5 6 HELIX 2 2 ASP A 1027 GLU A 1029 5 3 HELIX 3 3 ARG A 1030 LEU A 1037 1 8 HELIX 4 4 GLY A 1070 LEU A 1084 1 15 HELIX 5 5 GLY A 1118 PHE A 1123 5 6 HELIX 6 6 ASP A 1133 ILE A 1147 1 15 HELIX 7 7 TYR A 1163 GLU A 1167 5 5 HELIX 8 8 VAL A 1177 LYS A 1181 5 5 HELIX 9 9 GLY A 1182 MET A 1190 1 9 HELIX 10 10 GLU A 1198 SER A 1208 1 11 HELIX 11 11 MET A 1234 LEU A 1253 1 20 HELIX 12 12 THR F 2012 GLN F 2017 1 6 HELIX 13 13 ASP F 2027 ALA F 2036 1 10 HELIX 14 14 ILE F 2069 LEU F 2084 1 16 HELIX 15 15 GLY F 2118 PHE F 2123 5 6 HELIX 16 16 ASP F 2133 ILE F 2147 1 15 HELIX 17 17 MET F 2184 MET F 2190 1 7 HELIX 18 18 GLU F 2198 SER F 2208 1 11 HELIX 19 19 LYS F 2235 LEU F 2252 1 18 SHEET 1 A 9 ASP A1039 HIS A1047 0 SHEET 2 A 9 PHE A1050 LEU A1057 -1 O SER A1052 N ALA A1045 SHEET 3 A 9 LYS A1060 CYS A1065 -1 O VAL A1062 N ALA A1055 SHEET 4 A 9 LEU A1021 ILE A1023 1 N ILE A1023 O ILE A1063 SHEET 5 A 9 THR A1088 ALA A1097 1 O THR A1088 N ALA A1022 SHEET 6 A 9 ASN A1194 GLU A1196 -1 O TYR A1195 N GLY A1096 SHEET 7 A 9 THR A1151 SER A1159 1 N ALA A1157 O ASN A1194 SHEET 8 A 9 VAL A1107 LEU A1116 1 N VAL A1114 O THR A1156 SHEET 9 A 9 ALA A1130 VAL A1131 -1 O ALA A1130 N SER A1113 SHEET 1 B 8 ASP A1039 HIS A1047 0 SHEET 2 B 8 PHE A1050 LEU A1057 -1 O SER A1052 N ALA A1045 SHEET 3 B 8 LYS A1060 CYS A1065 -1 O VAL A1062 N ALA A1055 SHEET 4 B 8 LEU A1021 ILE A1023 1 N ILE A1023 O ILE A1063 SHEET 5 B 8 THR A1088 ALA A1097 1 O THR A1088 N ALA A1022 SHEET 6 B 8 ARG A1212 ASN A1222 1 O ARG A1212 N PHE A1089 SHEET 7 B 8 VAL A1107 LEU A1116 -1 N LEU A1108 O ALA A1217 SHEET 8 B 8 ALA A1130 VAL A1131 -1 O ALA A1130 N SER A1113 SHEET 1 C 8 ASP F2039 HIS F2047 0 SHEET 2 C 8 PHE F2050 LEU F2057 -1 O ARG F2054 N VAL F2042 SHEET 3 C 8 LYS F2060 CYS F2065 -1 O VAL F2062 N ALA F2055 SHEET 4 C 8 LEU F2021 ILE F2023 1 N ILE F2023 O ILE F2063 SHEET 5 C 8 THR F2088 GLY F2096 1 O THR F2088 N ALA F2022 SHEET 6 C 8 ARG F2212 VAL F2221 1 O ARG F2212 N PHE F2089 SHEET 7 C 8 VAL F2107 LEU F2116 -1 N LEU F2108 O ALA F2217 SHEET 8 C 8 ALA F2130 VAL F2131 -1 O ALA F2130 N SER F2113 SHEET 1 D 9 ASP F2039 HIS F2047 0 SHEET 2 D 9 PHE F2050 LEU F2057 -1 O ARG F2054 N VAL F2042 SHEET 3 D 9 LYS F2060 CYS F2065 -1 O VAL F2062 N ALA F2055 SHEET 4 D 9 LEU F2021 ILE F2023 1 N ILE F2023 O ILE F2063 SHEET 5 D 9 THR F2088 GLY F2096 1 O THR F2088 N ALA F2022 SHEET 6 D 9 ARG F2212 VAL F2221 1 O ARG F2212 N PHE F2089 SHEET 7 D 9 VAL F2107 LEU F2116 -1 N LEU F2108 O ALA F2217 SHEET 8 D 9 THR F2151 SER F2159 1 O HIS F2152 N VAL F2109 SHEET 9 D 9 ASN F2194 GLU F2196 1 O ASN F2194 N ALA F2157 SITE 1 AC1 7 ILE A1069 PHE A1162 HOH A3053 HOH A3100 SITE 2 AC1 7 HIS F2008 ARG F2048 HOH F3236 SITE 1 AC2 5 TYR A1172 SER A1173 ALA A1189 HOH A3226 SITE 2 AC2 5 GLN F2209 CRYST1 150.820 150.820 47.840 90.00 90.00 120.00 H 3 18 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 0.006630 0.003828 0.000000 0.00000 SCALE2 0.000000 0.007656 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020903 0.00000