HEADER ISOMERASE 19-FEB-08 2VOM TITLE STRUCTURAL BASIS OF HUMAN TRIOSEPHOSPHATE ISOMERASE DEFICIENCY. TITLE 2 MUTATION E104D AND CORRELATION TO SOLVENT PERTURBATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIOSEPHOSPHATE ISOMERASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: RESIDUES 2-249; COMPND 5 SYNONYM: TIM; COMPND 6 EC: 5.3.1.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3B KEYWDS ISOMERASE, ALTERNATIVE SPLICING, FATTY ACID BIOSYNTHESIS, LIPID KEYWDS 2 SYNTHESIS, DISEASE MUTATION, PENTOSE SHUNT, PHOSPHOPROTEIN, KEYWDS 3 GLUCONEOGENESIS, GLYCOLYSIS, ACETYLATION, POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR C.RODRIGUEZ-ALMAZAN,R.ARREOLA-ALEMON,D.RODRIGUEZ-LARREA,B.AGUIRRE- AUTHOR 2 LOPEZ,M.T.DE GOMEZ-PUYOU,R.PEREZ-MONTFORT,M.COSTAS,A.GOMEZ-PUYOU, AUTHOR 3 A.TORRES-LARIOS REVDAT 6 13-DEC-23 2VOM 1 REMARK REVDAT 5 29-SEP-09 2VOM 1 JRNL REMARK REVDAT 4 24-FEB-09 2VOM 1 VERSN REVDAT 3 26-AUG-08 2VOM 1 JRNL REVDAT 2 01-JUL-08 2VOM 1 JRNL REMARK REVDAT 1 17-JUN-08 2VOM 0 JRNL AUTH C.RODRIGUEZ-ALMAZAN,R.ARREOLA-ALEMON,D.RODRIGUEZ-LARREA, JRNL AUTH 2 B.AGUIRRE-LOPEZ,M.T.DE GOMEZ-PUYOU,R.PEREZ-MONTFORT, JRNL AUTH 3 M.COSTAS,A.GOMEZ-PUYOU,A.TORRES-LARIOS JRNL TITL STRUCTURAL BASIS OF HUMAN TRIOSEPHOSPHATE ISOMERASE JRNL TITL 2 DEFICIENCY: MUTATION E104D IS RELATED TO ALTERATIONS OF A JRNL TITL 3 CONSERVED WATER NETWORK AT THE DIMER INTERFACE. JRNL REF J.BIOL.CHEM. V. 283 23254 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18562316 JRNL DOI 10.1074/JBC.M802145200 REMARK 2 REMARK 2 RESOLUTION. 1.85 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 81958 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) : 0.219 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 4142 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7727 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.72 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 413 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7372 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 611 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.26500 REMARK 3 B22 (A**2) : 0.45000 REMARK 3 B33 (A**2) : -1.71500 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.14600 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) : 0.18 REMARK 3 LOW RESOLUTION CUTOFF (A) : 50.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.251 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.58 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 36.30 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 : CNS_TOPPARPROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : CNS_TOPPARWATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CHAIN D IS MORE DISORDERED THAN CHAINS REMARK 3 A, B AND C ON RESIDUES 1 THIS IS PROBABLY DUE TO LACK OF REMARK 3 CRYSTALLOGRAPHIC CONTACTS REMARK 4 REMARK 4 2VOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 19-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1290035383. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-07 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR REMARK 200 OPTICS : HIGH-RESOLUTION DOUBLE- CRYSTAL REMARK 200 SI(220) SAGITTAL FOCUSING, REMARK 200 ROSENBAUM-ROCK VERTICAL FOCUSING REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81960 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 60.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : 0.11000 REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.57 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : 0.32000 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1WYI REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS PH 8.5, 20% PEG MME2000, REMARK 280 4% POLYPROPYLENE GLYCOL P400, 10 MM NICL2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 160.26050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.64400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 160.26050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.64400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.3 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 350 REMARK 350 BIOMOLECULE: 2 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: 3380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 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 B2032 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 105 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN B, GLU 105 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN C, GLU 105 TO ASP REMARK 400 ENGINEERED RESIDUE IN CHAIN D, GLU 105 TO ASP 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 -1 REMARK 465 SER A 0 REMARK 465 ALA A 1 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 ALA B 1 REMARK 465 PRO B 2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 ALA C 1 REMARK 465 PRO C 2 REMARK 465 GLN C 248 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 ALA D 1 REMARK 465 PRO D 2 REMARK 465 SER D 3 REMARK 465 ALA D 246 REMARK 465 LYS D 247 REMARK 465 GLN D 248 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 LYS A 13 -149.15 55.94 REMARK 500 ALA A 136 4.09 -69.59 REMARK 500 VAL A 196 -76.39 -119.26 REMARK 500 LYS B 13 -146.07 53.88 REMARK 500 ASP B 36 54.31 -90.42 REMARK 500 ASN B 65 167.13 179.57 REMARK 500 THR B 172 -1.97 -152.35 REMARK 500 VAL B 196 -73.63 -122.71 REMARK 500 LYS C 13 -147.94 51.88 REMARK 500 PRO C 34 93.91 -56.27 REMARK 500 ALA C 35 -54.47 -12.15 REMARK 500 ASP C 36 10.16 -63.02 REMARK 500 ASN C 65 167.35 177.49 REMARK 500 THR C 172 -21.83 -152.91 REMARK 500 SER C 197 162.75 178.11 REMARK 500 LYS D 13 -147.30 46.93 REMARK 500 ASN D 65 165.64 178.56 REMARK 500 ALA D 136 9.33 -61.90 REMARK 500 SER D 194 -70.11 -72.04 REMARK 500 VAL D 196 -85.01 -118.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 700 THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WYI RELATED DB: PDB REMARK 900 HUMAN TRIOSEPHOSPHATE ISOMERASE OF NEW CRYSTAL FORM REMARK 900 RELATED ID: 1HTI RELATED DB: PDB REMARK 900 TRIOSEPHOSPHATE ISOMERASE (TIM) COMPLEXED WITH 2-PHOSPHOGLYCOLIC REMARK 900 ACID REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE STRUCTURE CORRESPONDS TO THE MUTANT E104D DBREF 2VOM A -1 0 PDB 2VOM 2VOM -1 0 DBREF 2VOM A 1 248 UNP P60174 TPIS_HUMAN 2 249 DBREF 2VOM B -1 0 PDB 2VOM 2VOM -1 0 DBREF 2VOM B 1 248 UNP P60174 TPIS_HUMAN 2 249 DBREF 2VOM C -1 0 PDB 2VOM 2VOM -1 0 DBREF 2VOM C 1 248 UNP P60174 TPIS_HUMAN 2 249 DBREF 2VOM D -1 0 PDB 2VOM 2VOM -1 0 DBREF 2VOM D 1 248 UNP P60174 TPIS_HUMAN 2 249 SEQADV 2VOM ASP A 104 UNP P60174 GLU 105 ENGINEERED MUTATION SEQADV 2VOM ASP B 104 UNP P60174 GLU 105 ENGINEERED MUTATION SEQADV 2VOM ASP C 104 UNP P60174 GLU 105 ENGINEERED MUTATION SEQADV 2VOM ASP D 104 UNP P60174 GLU 105 ENGINEERED MUTATION SEQRES 1 A 250 GLY SER ALA PRO SER ARG LYS PHE PHE VAL GLY GLY ASN SEQRES 2 A 250 TRP LYS MET ASN GLY ARG LYS GLN SER LEU GLY GLU LEU SEQRES 3 A 250 ILE GLY THR LEU ASN ALA ALA LYS VAL PRO ALA ASP THR SEQRES 4 A 250 GLU VAL VAL CYS ALA PRO PRO THR ALA TYR ILE ASP PHE SEQRES 5 A 250 ALA ARG GLN LYS LEU ASP PRO LYS ILE ALA VAL ALA ALA SEQRES 6 A 250 GLN ASN CYS TYR LYS VAL THR ASN GLY ALA PHE THR GLY SEQRES 7 A 250 GLU ILE SER PRO GLY MET ILE LYS ASP CYS GLY ALA THR SEQRES 8 A 250 TRP VAL VAL LEU GLY HIS SER GLU ARG ARG HIS VAL PHE SEQRES 9 A 250 GLY ASP SER ASP GLU LEU ILE GLY GLN LYS VAL ALA HIS SEQRES 10 A 250 ALA LEU ALA GLU GLY LEU GLY VAL ILE ALA CYS ILE GLY SEQRES 11 A 250 GLU LYS LEU ASP GLU ARG GLU ALA GLY ILE THR GLU LYS SEQRES 12 A 250 VAL VAL PHE GLU GLN THR LYS VAL ILE ALA ASP ASN VAL SEQRES 13 A 250 LYS ASP TRP SER LYS VAL VAL LEU ALA TYR GLU PRO VAL SEQRES 14 A 250 TRP ALA ILE GLY THR GLY LYS THR ALA THR PRO GLN GLN SEQRES 15 A 250 ALA GLN GLU VAL HIS GLU LYS LEU ARG GLY TRP LEU LYS SEQRES 16 A 250 SER ASN VAL SER ASP ALA VAL ALA GLN SER THR ARG ILE SEQRES 17 A 250 ILE TYR GLY GLY SER VAL THR GLY ALA THR CYS LYS GLU SEQRES 18 A 250 LEU ALA SER GLN PRO ASP VAL ASP GLY PHE LEU VAL GLY SEQRES 19 A 250 GLY ALA SER LEU LYS PRO GLU PHE VAL ASP ILE ILE ASN SEQRES 20 A 250 ALA LYS GLN SEQRES 1 B 250 GLY SER ALA PRO SER ARG LYS PHE PHE VAL GLY GLY ASN SEQRES 2 B 250 TRP LYS MET ASN GLY ARG LYS GLN SER LEU GLY GLU LEU SEQRES 3 B 250 ILE GLY THR LEU ASN ALA ALA LYS VAL PRO ALA ASP THR SEQRES 4 B 250 GLU VAL VAL CYS ALA PRO PRO THR ALA TYR ILE ASP PHE SEQRES 5 B 250 ALA ARG GLN LYS LEU ASP PRO LYS ILE ALA VAL ALA ALA SEQRES 6 B 250 GLN ASN CYS TYR LYS VAL THR ASN GLY ALA PHE THR GLY SEQRES 7 B 250 GLU ILE SER PRO GLY MET ILE LYS ASP CYS GLY ALA THR SEQRES 8 B 250 TRP VAL VAL LEU GLY HIS SER GLU ARG ARG HIS VAL PHE SEQRES 9 B 250 GLY ASP SER ASP GLU LEU ILE GLY GLN LYS VAL ALA HIS SEQRES 10 B 250 ALA LEU ALA GLU GLY LEU GLY VAL ILE ALA CYS ILE GLY SEQRES 11 B 250 GLU LYS LEU ASP GLU ARG GLU ALA GLY ILE THR GLU LYS SEQRES 12 B 250 VAL VAL PHE GLU GLN THR LYS VAL ILE ALA ASP ASN VAL SEQRES 13 B 250 LYS ASP TRP SER LYS VAL VAL LEU ALA TYR GLU PRO VAL SEQRES 14 B 250 TRP ALA ILE GLY THR GLY LYS THR ALA THR PRO GLN GLN SEQRES 15 B 250 ALA GLN GLU VAL HIS GLU LYS LEU ARG GLY TRP LEU LYS SEQRES 16 B 250 SER ASN VAL SER ASP ALA VAL ALA GLN SER THR ARG ILE SEQRES 17 B 250 ILE TYR GLY GLY SER VAL THR GLY ALA THR CYS LYS GLU SEQRES 18 B 250 LEU ALA SER GLN PRO ASP VAL ASP GLY PHE LEU VAL GLY SEQRES 19 B 250 GLY ALA SER LEU LYS PRO GLU PHE VAL ASP ILE ILE ASN SEQRES 20 B 250 ALA LYS GLN SEQRES 1 C 250 GLY SER ALA PRO SER ARG LYS PHE PHE VAL GLY GLY ASN SEQRES 2 C 250 TRP LYS MET ASN GLY ARG LYS GLN SER LEU GLY GLU LEU SEQRES 3 C 250 ILE GLY THR LEU ASN ALA ALA LYS VAL PRO ALA ASP THR SEQRES 4 C 250 GLU VAL VAL CYS ALA PRO PRO THR ALA TYR ILE ASP PHE SEQRES 5 C 250 ALA ARG GLN LYS LEU ASP PRO LYS ILE ALA VAL ALA ALA SEQRES 6 C 250 GLN ASN CYS TYR LYS VAL THR ASN GLY ALA PHE THR GLY SEQRES 7 C 250 GLU ILE SER PRO GLY MET ILE LYS ASP CYS GLY ALA THR SEQRES 8 C 250 TRP VAL VAL LEU GLY HIS SER GLU ARG ARG HIS VAL PHE SEQRES 9 C 250 GLY ASP SER ASP GLU LEU ILE GLY GLN LYS VAL ALA HIS SEQRES 10 C 250 ALA LEU ALA GLU GLY LEU GLY VAL ILE ALA CYS ILE GLY SEQRES 11 C 250 GLU LYS LEU ASP GLU ARG GLU ALA GLY ILE THR GLU LYS SEQRES 12 C 250 VAL VAL PHE GLU GLN THR LYS VAL ILE ALA ASP ASN VAL SEQRES 13 C 250 LYS ASP TRP SER LYS VAL VAL LEU ALA TYR GLU PRO VAL SEQRES 14 C 250 TRP ALA ILE GLY THR GLY LYS THR ALA THR PRO GLN GLN SEQRES 15 C 250 ALA GLN GLU VAL HIS GLU LYS LEU ARG GLY TRP LEU LYS SEQRES 16 C 250 SER ASN VAL SER ASP ALA VAL ALA GLN SER THR ARG ILE SEQRES 17 C 250 ILE TYR GLY GLY SER VAL THR GLY ALA THR CYS LYS GLU SEQRES 18 C 250 LEU ALA SER GLN PRO ASP VAL ASP GLY PHE LEU VAL GLY SEQRES 19 C 250 GLY ALA SER LEU LYS PRO GLU PHE VAL ASP ILE ILE ASN SEQRES 20 C 250 ALA LYS GLN SEQRES 1 D 250 GLY SER ALA PRO SER ARG LYS PHE PHE VAL GLY GLY ASN SEQRES 2 D 250 TRP LYS MET ASN GLY ARG LYS GLN SER LEU GLY GLU LEU SEQRES 3 D 250 ILE GLY THR LEU ASN ALA ALA LYS VAL PRO ALA ASP THR SEQRES 4 D 250 GLU VAL VAL CYS ALA PRO PRO THR ALA TYR ILE ASP PHE SEQRES 5 D 250 ALA ARG GLN LYS LEU ASP PRO LYS ILE ALA VAL ALA ALA SEQRES 6 D 250 GLN ASN CYS TYR LYS VAL THR ASN GLY ALA PHE THR GLY SEQRES 7 D 250 GLU ILE SER PRO GLY MET ILE LYS ASP CYS GLY ALA THR SEQRES 8 D 250 TRP VAL VAL LEU GLY HIS SER GLU ARG ARG HIS VAL PHE SEQRES 9 D 250 GLY ASP SER ASP GLU LEU ILE GLY GLN LYS VAL ALA HIS SEQRES 10 D 250 ALA LEU ALA GLU GLY LEU GLY VAL ILE ALA CYS ILE GLY SEQRES 11 D 250 GLU LYS LEU ASP GLU ARG GLU ALA GLY ILE THR GLU LYS SEQRES 12 D 250 VAL VAL PHE GLU GLN THR LYS VAL ILE ALA ASP ASN VAL SEQRES 13 D 250 LYS ASP TRP SER LYS VAL VAL LEU ALA TYR GLU PRO VAL SEQRES 14 D 250 TRP ALA ILE GLY THR GLY LYS THR ALA THR PRO GLN GLN SEQRES 15 D 250 ALA GLN GLU VAL HIS GLU LYS LEU ARG GLY TRP LEU LYS SEQRES 16 D 250 SER ASN VAL SER ASP ALA VAL ALA GLN SER THR ARG ILE SEQRES 17 D 250 ILE TYR GLY GLY SER VAL THR GLY ALA THR CYS LYS GLU SEQRES 18 D 250 LEU ALA SER GLN PRO ASP VAL ASP GLY PHE LEU VAL GLY SEQRES 19 D 250 GLY ALA SER LEU LYS PRO GLU PHE VAL ASP ILE ILE ASN SEQRES 20 D 250 ALA LYS GLN FORMUL 5 HOH *611(H2 O) HELIX 1 1 ARG A 17 ALA A 31 1 15 HELIX 2 2 PRO A 44 ALA A 46 5 3 HELIX 3 3 TYR A 47 LEU A 55 1 9 HELIX 4 4 SER A 79 CYS A 86 1 8 HELIX 5 5 HIS A 95 VAL A 101 1 7 HELIX 6 6 SER A 105 GLU A 119 1 15 HELIX 7 7 LYS A 130 ALA A 136 1 7 HELIX 8 8 ILE A 138 ASN A 153 1 16 HELIX 9 9 ASP A 156 SER A 158 5 3 HELIX 10 10 PRO A 166 ILE A 170 5 5 HELIX 11 11 THR A 177 VAL A 196 1 20 HELIX 12 12 SER A 197 THR A 204 1 8 HELIX 13 13 THR A 216 SER A 222 1 7 HELIX 14 14 GLY A 232 LYS A 237 5 6 HELIX 15 15 PRO A 238 ASN A 245 1 8 HELIX 16 16 ARG B 17 ALA B 31 1 15 HELIX 17 17 PRO B 44 ALA B 46 5 3 HELIX 18 18 TYR B 47 LEU B 55 1 9 HELIX 19 19 SER B 79 CYS B 86 1 8 HELIX 20 20 HIS B 95 VAL B 101 1 7 HELIX 21 21 SER B 105 GLU B 119 1 15 HELIX 22 22 LYS B 130 ALA B 136 1 7 HELIX 23 23 ILE B 138 ASP B 152 1 15 HELIX 24 24 ASP B 156 SER B 158 5 3 HELIX 25 25 THR B 177 VAL B 196 1 20 HELIX 26 26 SER B 197 THR B 204 1 8 HELIX 27 27 THR B 216 GLN B 223 1 8 HELIX 28 28 GLY B 232 LYS B 237 5 6 HELIX 29 29 PRO B 238 ASN B 245 1 8 HELIX 30 30 ARG C 17 ALA C 31 1 15 HELIX 31 31 PRO C 44 ALA C 46 5 3 HELIX 32 32 TYR C 47 LEU C 55 1 9 HELIX 33 33 SER C 79 CYS C 86 1 8 HELIX 34 34 HIS C 95 VAL C 101 1 7 HELIX 35 35 SER C 105 GLU C 119 1 15 HELIX 36 36 LYS C 130 ALA C 136 1 7 HELIX 37 37 ILE C 138 ASP C 152 1 15 HELIX 38 38 ASP C 156 SER C 158 5 3 HELIX 39 39 THR C 177 VAL C 196 1 20 HELIX 40 40 SER C 197 THR C 204 1 8 HELIX 41 41 THR C 216 SER C 222 1 7 HELIX 42 42 GLY C 232 LYS C 237 5 6 HELIX 43 43 PRO C 238 ASN C 245 1 8 HELIX 44 44 ARG D 17 ALA D 31 1 15 HELIX 45 45 PRO D 44 ALA D 46 5 3 HELIX 46 46 TYR D 47 LEU D 55 1 9 HELIX 47 47 SER D 79 CYS D 86 1 8 HELIX 48 48 HIS D 95 VAL D 101 1 7 HELIX 49 49 SER D 105 GLU D 119 1 15 HELIX 50 50 LYS D 130 ALA D 136 1 7 HELIX 51 51 ILE D 138 ASP D 152 1 15 HELIX 52 52 ASP D 156 SER D 158 5 3 HELIX 53 53 THR D 177 VAL D 196 1 20 HELIX 54 54 SER D 197 THR D 204 1 8 HELIX 55 55 THR D 216 SER D 222 1 7 HELIX 56 56 GLY D 232 LYS D 237 5 6 HELIX 57 57 PRO D 238 ILE D 244 1 7 SHEET 1 AA10 PHE A 6 ASN A 11 0 SHEET 2 AA10 THR A 37 ALA A 42 1 O GLU A 38 N VAL A 8 SHEET 3 AA10 ALA A 60 ALA A 63 1 O ALA A 60 N CYS A 41 SHEET 4 AA10 TRP A 90 LEU A 93 1 O TRP A 90 N ALA A 63 SHEET 5 AA10 GLY A 122 ILE A 127 1 O GLY A 122 N VAL A 91 SHEET 6 AA10 VAL A 160 TYR A 164 1 O VAL A 161 N ALA A 125 SHEET 7 AA10 ARG A 205 TYR A 208 1 O ARG A 205 N LEU A 162 SHEET 8 AA10 GLY A 228 VAL A 231 1 O GLY A 228 N TYR A 208 SHEET 9 AA10 PHE A 6 ASN A 11 1 O PHE A 7 N PHE A 229 SHEET 10 AA10 PHE A 6 ASN A 11 0 SHEET 1 BA10 PHE B 6 ASN B 11 0 SHEET 2 BA10 THR B 37 ALA B 42 1 O GLU B 38 N VAL B 8 SHEET 3 BA10 ALA B 60 ALA B 63 1 O ALA B 60 N CYS B 41 SHEET 4 BA10 TRP B 90 LEU B 93 1 O TRP B 90 N ALA B 63 SHEET 5 BA10 GLY B 122 ILE B 127 1 O GLY B 122 N VAL B 91 SHEET 6 BA10 VAL B 160 TYR B 164 1 O VAL B 161 N ALA B 125 SHEET 7 BA10 ILE B 206 TYR B 208 1 O ILE B 207 N TYR B 164 SHEET 8 BA10 GLY B 228 VAL B 231 1 O GLY B 228 N TYR B 208 SHEET 9 BA10 PHE B 6 ASN B 11 1 O PHE B 7 N PHE B 229 SHEET 10 BA10 PHE B 6 ASN B 11 0 SHEET 1 CA22 PHE C 6 ASN C 11 0 SHEET 2 CA22 THR C 37 ALA C 42 1 O GLU C 38 N VAL C 8 SHEET 3 CA22 ALA C 60 ALA C 63 1 O ALA C 60 N CYS C 41 SHEET 4 CA22 TRP C 90 LEU C 93 1 O TRP C 90 N ALA C 63 SHEET 5 CA22 GLY C 122 ILE C 127 1 O GLY C 122 N VAL C 91 SHEET 6 CA22 VAL C 160 TYR C 164 1 O VAL C 161 N ALA C 125 SHEET 7 CA22 ILE C 206 TYR C 208 1 O ILE C 207 N TYR C 164 SHEET 8 CA22 GLY C 228 VAL C 231 1 O GLY C 228 N TYR C 208 SHEET 9 CA22 THR C 37 ALA C 42 0 SHEET 10 CA22 PHE C 6 ASN C 11 1 O PHE C 6 N GLU C 38 SHEET 11 CA22 ALA C 60 ALA C 63 0 SHEET 12 CA22 THR C 37 ALA C 42 1 O VAL C 39 N ALA C 60 SHEET 13 CA22 TRP C 90 LEU C 93 0 SHEET 14 CA22 ALA C 60 ALA C 63 1 O ALA C 63 N VAL C 92 SHEET 15 CA22 GLY C 122 ILE C 127 0 SHEET 16 CA22 TRP C 90 LEU C 93 1 O VAL C 91 N ILE C 124 SHEET 17 CA22 VAL C 160 TYR C 164 0 SHEET 18 CA22 GLY C 122 ILE C 127 1 O VAL C 123 N VAL C 161 SHEET 19 CA22 ILE C 206 TYR C 208 0 SHEET 20 CA22 VAL C 160 TYR C 164 1 O LEU C 162 N ILE C 207 SHEET 21 CA22 GLY C 228 VAL C 231 0 SHEET 22 CA22 PHE C 6 ASN C 11 1 O PHE C 7 N PHE C 229 SHEET 1 DA16 PHE D 6 ASN D 11 0 SHEET 2 DA16 THR D 37 ALA D 42 1 O GLU D 38 N VAL D 8 SHEET 3 DA16 THR D 37 ALA D 42 1 O THR D 37 N VAL D 39 SHEET 4 DA16 PHE D 6 ASN D 11 1 O PHE D 6 N GLU D 38 SHEET 5 DA16 ALA D 60 ALA D 63 0 SHEET 6 DA16 THR D 37 ALA D 42 1 O VAL D 39 N ALA D 60 SHEET 7 DA16 TRP D 90 LEU D 93 0 SHEET 8 DA16 ALA D 60 ALA D 63 1 O ALA D 63 N VAL D 92 SHEET 9 DA16 GLY D 122 ILE D 127 0 SHEET 10 DA16 TRP D 90 LEU D 93 1 O VAL D 91 N ILE D 124 SHEET 11 DA16 VAL D 160 TYR D 164 0 SHEET 12 DA16 GLY D 122 ILE D 127 1 O VAL D 123 N VAL D 161 SHEET 13 DA16 ILE D 206 TYR D 208 0 SHEET 14 DA16 VAL D 160 TYR D 164 1 O LEU D 162 N ILE D 207 SHEET 15 DA16 GLY D 228 VAL D 231 0 SHEET 16 DA16 PHE D 6 ASN D 11 1 O PHE D 7 N PHE D 229 CRYST1 320.521 47.288 68.957 90.00 97.20 90.00 C 1 2 1 16 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 0.003120 0.000000 0.000394 0.00000 SCALE2 0.000000 0.021147 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014617 0.00000 MTRIX1 1 -0.631240 0.344010 -0.695120 -8.66865 1 MTRIX2 1 0.323280 -0.697980 -0.639000 -4.32283 1 MTRIX3 1 -0.705000 -0.628080 0.329380 -6.54332 1 MTRIX1 2 -0.008650 0.774900 -0.632030 -27.01038 1 MTRIX2 2 -0.992850 0.068590 0.097690 -37.60305 1 MTRIX3 2 0.119050 0.628350 0.768760 36.36592 1 MTRIX1 3 0.706700 -0.121930 -0.696920 -25.58899 1 MTRIX2 3 0.590540 -0.440850 0.675950 -29.65629 1 MTRIX3 3 -0.389660 -0.889260 -0.239550 27.95633 1