HEADER TRANSFERASE 26-OCT-07 2VET TITLE CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH DUMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TS, TSASE,; COMPND 5 EC: 2.1.1.45; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: DUMP\: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 511693; SOURCE 4 STRAIN: BL21; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS REPRESSOR, CYTOPLASM, RNA-BINDING, TRANSFERASE, NUCLEOTIDE KEYWDS 2 BIOSYNTHESIS, DUMP SUBSTRATE, METHYLTRANSFERASE, THYMIDYLATE KEYWDS 3 SYNTHASE, TRANSLATION REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR R.R.SOTELO-MUNDO,R.ARREOLA,F.MALEY,W.R.MONTFORT REVDAT 5 13-DEC-23 2VET 1 LINK REVDAT 4 12-JUL-17 2VET 1 REVDAT 3 24-FEB-09 2VET 1 VERSN REVDAT 2 05-AUG-08 2VET 1 COMPND SOURCE KEYWDS JRNL REVDAT 2 2 1 REMARK REVDAT 1 04-DEC-07 2VET 0 JRNL AUTH A.A.ARVIZU-FLORES,R.SUGICH-MIRANDA,R.ARREOLA, JRNL AUTH 2 K.D.GARCIA-OROZCO,E.F.VELAZQUEZ-CONTRERAS,W.R.MONTFORT, JRNL AUTH 3 F.MALEY,R.R.SOTELO-MUNDO JRNL TITL ROLE OF AN INVARIANT LYSINE RESIDUE IN FOLATE BINDING ON JRNL TITL 2 ESCHERICHIA COLI THYMIDYLATE SYNTHASE: CALORIMETRIC AND JRNL TITL 3 CRYSTALLOGRAPHIC ANALYSIS OF THE K48Q MUTANT. JRNL REF INT.J.BIOCHEM.CELL BIOL. V. 40 2206 2008 JRNL REFN ISSN 1357-2725 JRNL PMID 18403248 JRNL DOI 10.1016/J.BIOCEL.2008.02.025 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 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 : MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 7243279.450 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 18173 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) : 0.185 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1426 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2290 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE : 0.2460 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 175 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2150 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 23 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.25 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.220 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) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.940 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.190 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.280 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 48.33 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : LIGAND.PAR REMARK 3 PARAMETER FILE 4 : DU3.PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : LIGAND2.TOP REMARK 3 TOPOLOGY FILE 4 : DU3.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2VET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1290034228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNESS, PROCOR REMARK 200 DATA SCALING SOFTWARE : AGROVATA, ROTAVATA, SCALA, REMARK 200 TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21347 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 95.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 76.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRIES 1FFL AND 1FWM REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE BUFFER, 4 MM REMARK 280 DTT AND INCREMENTS IN AMMONIUM SULFATE FROM 2.05 TO 2.6 M, PH REMARK 280 7.5 TO 8 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z+1/2,-X+1/2,-Y REMARK 290 7555 -Z+1/2,-X,Y+1/2 REMARK 290 8555 -Z,X+1/2,-Y+1/2 REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z+1/2,-X+1/2 REMARK 290 11555 Y+1/2,-Z+1/2,-X REMARK 290 12555 -Y+1/2,-Z,X+1/2 REMARK 290 13555 X+1/2,Y+1/2,Z+1/2 REMARK 290 14555 -X,-Y+1/2,Z REMARK 290 15555 -X+1/2,Y,-Z REMARK 290 16555 X,-Y,-Z+1/2 REMARK 290 17555 Z+1/2,X+1/2,Y+1/2 REMARK 290 18555 Z,-X,-Y+1/2 REMARK 290 19555 -Z,-X+1/2,Y REMARK 290 20555 -Z+1/2,X,-Y REMARK 290 21555 Y+1/2,Z+1/2,X+1/2 REMARK 290 22555 -Y+1/2,Z,-X REMARK 290 23555 Y,-Z,-X+1/2 REMARK 290 24555 -Y,-Z+1/2,X 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 66.43500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.43500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.43500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.43500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.43500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 66.43500 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 66.43500 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 66.43500 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 66.43500 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 66.43500 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 66.43500 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 66.43500 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 66.43500 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.43500 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 66.43500 REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 66.43500 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 66.43500 REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 66.43500 REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 66.43500 REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 66.43500 REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 66.43500 REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 66.43500 REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 66.43500 REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 66.43500 REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 66.43500 REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 66.43500 REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 5410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.43500 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2023 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 48 TO GLN 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 N MET A 1 O2 FMT A 1265 2.18 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 VAL A 93 -169.18 -75.14 REMARK 500 TYR A 94 -71.67 -21.25 REMARK 500 ALA A 100 53.45 -150.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (UMP): UMP OR DUMP IS THE REMARK 600 SUBSTRATE MOLECULE REMARK 600 CARBOXY GROUP (CBX): CBX IS LINKED TO MET1 FORMING A REMARK 600 N-FORMYLMETHIONINE REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT A1265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMP A1266 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JG0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASECOMPLEXED REMARK 900 WITH 2'- DEOXYURIDINE-5'-MONOPHOSPHATE AND N,O- DIDANSYL-L-TYROSINE REMARK 900 RELATED ID: 1BID RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DUMP REMARK 900 RELATED ID: 1JTU RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN A COMPLEX WITH DUMP ANDLY338913, A REMARK 900 POLYGLUTAMYLATED PYRROLO(2,3-D)PYRIMIDINE-BASED ANTIFOLATE REMARK 900 RELATED ID: 1DDU RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2',5'- REMARK 900 DIDEOXYURIDINE (DDURD) REMARK 900 RELATED ID: 1BJG RELATED DB: PDB REMARK 900 D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR REMARK 900 IMIDAZOLIDINE RING REMARK 900 RELATED ID: 1AXW RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND REMARK 900 2'-DEOXYURIDINE 5'- MONOPHOSPHATE (DUMP) REMARK 900 RELATED ID: 2FTQ RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE AT 1.8 A RESOLUTION REMARK 900 RELATED ID: 1SYN RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH BW1843U89 AND 2'- REMARK 900 DEOXYURIDINE 5'- MONOPHOSPHATE (DUMP) REMARK 900 RELATED ID: 1TSD RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE COMPLEX WITH 2'- DEOXYURIDINE 5'-MONOPHOSPHATE REMARK 900 (DUMP) AND FOLATE ANALOG 1843U89 REMARK 900 RELATED ID: 1FFL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE APO-THYMIDYLATE SYNTHASE R166QMUTANT REMARK 900 RELATED ID: 1BQ1 RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 REMARK 900 AND 2'-DEOXYURIDINE 5 '-MONOPHOSPHATE (DUMP) REMARK 900 RELATED ID: 2KCE RELATED DB: PDB REMARK 900 BINDING OF THE ANTICANCER DRUG ZD1694 TO E . COLI THYMIDYLATE REMARK 900 SYNTHASE: ASSESSING SPECIFICITY AND AFFINITY REMARK 900 RELATED ID: 1EVF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI REMARK 900 RELATED ID: 2FTN RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE Y94F MUTANT REMARK 900 RELATED ID: 1DNA RELATED DB: PDB REMARK 900 D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR REMARK 900 IMIDAZOLIDINE RING REMARK 900 RELATED ID: 1KCE RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE MUTANT E58Q IN COMPLEX WITH CB3717 AND REMARK 900 2'-DEOXYURIDINE 5 '-MONOPHOSPHATE (DUMP) REMARK 900 RELATED ID: 1JTQ RELATED DB: PDB REMARK 900 E. COLI TS COMPLEX WITH DUMP AND THE PYRROLO(2,3-D)PYRIMIDINE-BASED REMARK 900 ANTIFOLATE LY341770 REMARK 900 RELATED ID: 1F4G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXEDWITH SP- REMARK 900 876 REMARK 900 RELATED ID: 1F4F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXEDWITH SP- REMARK 900 722 REMARK 900 RELATED ID: 1TJS RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE REMARK 900 RELATED ID: 1FWM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE R166Q MUTANT REMARK 900 RELATED ID: 1AN5 RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 REMARK 900 RELATED ID: 1F4C RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASECOVALENTLY REMARK 900 MODIFIED AT C146 WITH N-[ TOSYL-D-PROLINYL]AMINO-ETHANETHIOL REMARK 900 RELATED ID: 1KZJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ECTS W80G/DUMP/CB3717 COMPLEX REMARK 900 RELATED ID: 1TRG RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN SYMMETRIC COMPLEX WITH CB3717 AND 2' REMARK 900 -DEOXYURIDINE 5'- MONOPHOSPHATE (DUMP) REMARK 900 RELATED ID: 2BBQ RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE COMPLEX WITH D-UMP AND POLYGLUTAMYL CB3717 REMARK 900 RELATED ID: 2G8O RELATED DB: PDB REMARK 900 HIGH RESOLUTION STRUCTURE OF ESCHERICHIA COLI THYMIDYLATESYNTHASE REMARK 900 TERNARY COMPLEX WITH DUMP AND A COFACTOR ANALOG,CB3717 REMARK 900 RELATED ID: 1TYS RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE MUTANT WITH CYS 146 REPLACED BY SER (C146S) REMARK 900 RELATED ID: 1NCE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A TERNARY COMPLEX OF E. COLITHYMIDYLATE REMARK 900 SYNTHASE D169C WITH DUMP AND THE ANTIFOLATECB3717 REMARK 900 RELATED ID: 1JUT RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE BOUND TO DUMP AND LY338529, APYRROLO(2, REMARK 900 3-D)PYRIMIDINE- BASED ANTIFOLATE REMARK 900 RELATED ID: 1TLC RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE COMPLEXED WITH DGMP AND FOLATE ANALOG 1843U89 REMARK 900 RELATED ID: 2G8X RELATED DB: PDB REMARK 900 ESCHERICHIA COLI Y209W APOPROTEIN REMARK 900 RELATED ID: 1EVG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI REMARK 900 WITH UNMODIFIED CATALYTIC CYSTEINE REMARK 900 RELATED ID: 1QQQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF SER254 MUTANT OF ESCHERICHIA COLI REMARK 900 THYMIDYLATE SYNTHASE REMARK 900 RELATED ID: 1EV8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF CYS167 MUTANT OF ESCHERICHIA COLI REMARK 900 RELATED ID: 1TLS RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND REMARK 900 METHYLENETETRAHYDROFOLATE REMARK 900 RELATED ID: 1F4B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ESCHERICHIA COLI THYMIDYLATE SYNTHASE REMARK 900 RELATED ID: 1ZPR RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE MUTANT E58Q IN COMPLEX WITH CB3717 AND REMARK 900 2'-DEOXYURIDINE 5 '-MONOPHOSPHATE (DUMP) REMARK 900 RELATED ID: 2FTO RELATED DB: PDB REMARK 900 Y94F MUTANT OF THYMIDYLATE SYNTHASE BOUND TO THYMIDINE-5'-PHOSPHATE REMARK 900 AND 10-PROPARGYL-5 ,8-DIDEAZAFOLID ACID REMARK 900 RELATED ID: 1KZI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ECTS/DUMP/THF COMPLEX REMARK 900 RELATED ID: 1F4E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE COMPLEXEDWITH REMARK 900 TOSYL-D-PROLINE REMARK 900 RELATED ID: 1BDU RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DURD REMARK 900 RELATED ID: 3TMS RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE REMARK 900 RELATED ID: 2A9W RELATED DB: PDB REMARK 900 E. COLI TS COMPLEXED WITH DUMP AND INHIBITOR GA9 REMARK 900 RELATED ID: 1TDU RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'- REMARK 900 DEOXYURIDINE (DURD) REMARK 900 RELATED ID: 2G8M RELATED DB: PDB REMARK 900 ESCHERICHIA COLI THYMIDYLATE SYNTHASE Y209W IN COMPLEX REMARK 900 WITHSUBSTRATE, DUMP, AND A COFACTOR ANALOG, CB3717 REMARK 900 RELATED ID: 1AOB RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE COMPLEXED WITH DDURD REMARK 900 RELATED ID: 1BQ2 RELATED DB: PDB REMARK 900 E. COLI THYMIDYLATE SYNTHASE MUTANT N177A REMARK 900 RELATED ID: 1AIQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT REMARK 900 RELATED ID: 1F4D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI THYMIDYLATE SYNTHASE C146S,L143C REMARK 900 COVALENTLY MODIFIED AT C143 WITH N-[TOSYL-D-PROLINYL]AMINO- REMARK 900 ETHANETHIOL REMARK 900 RELATED ID: 1EV5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE ANALYSIS OF ALA167 MUTANT OF ESCHERICHIA COLI REMARK 900 RELATED ID: 1AJM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE R126E MUTANT REMARK 900 RELATED ID: 2TSC RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE COMPLEX WITH DUMP AND AN ANTI-FOLATE (CB3717) REMARK 900 RELATED ID: 1TSN RELATED DB: PDB REMARK 900 THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH FDUMP AND REMARK 900 METHYLENETETRAHYDROFOLATE REMARK 900 RELATED ID: 2VF0 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q COMPLEXED WITH REMARK 900 5NO2DUMP AND BW1843U89 REMARK 900 RELATED ID: 3B5B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE THYMIDYLATE SYNTHASE K48Q MUTANT K48Q REMARK 900 COMPLEXED WITH 5NO2DUMP DBREF 2VET A 1 264 UNP P0A884 TYSY_ECOLI 1 264 SEQADV 2VET GLN A 48 UNP P0A884 LYS 48 ENGINEERED MUTATION SEQRES 1 A 264 MET LYS GLN TYR LEU GLU LEU MET GLN LYS VAL LEU ASP SEQRES 2 A 264 GLU GLY THR GLN LYS ASN ASP ARG THR GLY THR GLY THR SEQRES 3 A 264 LEU SER ILE PHE GLY HIS GLN MET ARG PHE ASN LEU GLN SEQRES 4 A 264 ASP GLY PHE PRO LEU VAL THR THR GLN ARG CYS HIS LEU SEQRES 5 A 264 ARG SER ILE ILE HIS GLU LEU LEU TRP PHE LEU GLN GLY SEQRES 6 A 264 ASP THR ASN ILE ALA TYR LEU HIS GLU ASN ASN VAL THR SEQRES 7 A 264 ILE TRP ASP GLU TRP ALA ASP GLU ASN GLY ASP LEU GLY SEQRES 8 A 264 PRO VAL TYR GLY LYS GLN TRP ARG ALA TRP PRO THR PRO SEQRES 9 A 264 ASP GLY ARG HIS ILE ASP GLN ILE THR THR VAL LEU ASN SEQRES 10 A 264 GLN LEU LYS ASN ASP PRO ASP SER ARG ARG ILE ILE VAL SEQRES 11 A 264 SER ALA TRP ASN VAL GLY GLU LEU ASP LYS MET ALA LEU SEQRES 12 A 264 ALA PRO CYS HIS ALA PHE PHE GLN PHE TYR VAL ALA ASP SEQRES 13 A 264 GLY LYS LEU SER CYS GLN LEU TYR GLN ARG SER CYS ASP SEQRES 14 A 264 VAL PHE LEU GLY LEU PRO PHE ASN ILE ALA SER TYR ALA SEQRES 15 A 264 LEU LEU VAL HIS MET MET ALA GLN GLN CYS ASP LEU GLU SEQRES 16 A 264 VAL GLY ASP PHE VAL TRP THR GLY GLY ASP THR HIS LEU SEQRES 17 A 264 TYR SER ASN HIS MET ASP GLN THR HIS LEU GLN LEU SER SEQRES 18 A 264 ARG GLU PRO ARG PRO LEU PRO LYS LEU ILE ILE LYS ARG SEQRES 19 A 264 LYS PRO GLU SER ILE PHE ASP TYR ARG PHE GLU ASP PHE SEQRES 20 A 264 GLU ILE GLU GLY TYR ASP PRO HIS PRO GLY ILE LYS ALA SEQRES 21 A 264 PRO VAL ALA ILE HET FMT A1265 3 HET UMP A1266 20 HETNAM FMT FORMIC ACID HETNAM UMP 2'-DEOXYURIDINE 5'-MONOPHOSPHATE HETSYN UMP DUMP FORMUL 2 FMT C H2 O2 FORMUL 3 UMP C9 H13 N2 O8 P FORMUL 4 HOH *44(H2 O) HELIX 1 1 MET A 1 GLY A 15 1 15 HELIX 2 2 GLN A 39 GLY A 41 5 3 HELIX 3 3 HIS A 51 GLY A 65 1 15 HELIX 4 4 ILE A 69 ASN A 75 1 7 HELIX 5 5 VAL A 93 ALA A 100 1 8 HELIX 6 6 ASP A 110 ASP A 122 1 13 HELIX 7 7 ASN A 134 MET A 141 5 8 HELIX 8 8 GLY A 173 ASP A 193 1 21 HELIX 9 9 HIS A 212 SER A 221 1 10 HELIX 10 10 ARG A 243 GLU A 245 5 3 SHEET 1 AA 6 THR A 16 ASN A 19 0 SHEET 2 AA 6 GLY A 25 ASN A 37 -1 O THR A 26 N LYS A 18 SHEET 3 AA 6 GLU A 195 TYR A 209 -1 O PHE A 199 N PHE A 36 SHEET 4 AA 6 LYS A 158 ASP A 169 1 O LEU A 159 N GLY A 197 SHEET 5 AA 6 HIS A 147 ALA A 155 -1 O PHE A 149 N TYR A 164 SHEET 6 AA 6 ILE A 129 SER A 131 -1 O VAL A 130 N PHE A 150 SHEET 1 AB 2 TRP A 101 PRO A 102 0 SHEET 2 AB 2 HIS A 108 ILE A 109 -1 O ILE A 109 N TRP A 101 SHEET 1 AC 2 LYS A 229 ILE A 232 0 SHEET 2 AC 2 PHE A 247 GLU A 250 -1 O GLU A 248 N ILE A 231 LINK N MET A 1 C FMT A1265 1555 1555 1.34 SITE 1 AC1 5 MET A 1 VAL A 45 THR A 46 THR A 47 SITE 2 AC1 5 HOH A2043 SITE 1 AC2 14 ARG A 21 ARG A 126 ARG A 127 CYS A 146 SITE 2 AC2 14 HIS A 147 GLN A 165 ARG A 166 SER A 167 SITE 3 AC2 14 CYS A 168 ASP A 169 ASN A 177 HIS A 207 SITE 4 AC2 14 TYR A 209 HOH A2044 CRYST1 132.870 132.870 132.870 90.00 90.00 90.00 I 21 3 24 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 0.007526 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007526 0.00000