HEADER OXIDOREDUCTASE 08-JAN-01 1HJ6 TITLE ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH ISOPROPYLMALATE, TITLE 2 NADP+ AND MAGNESIUM (FLASH-COOLED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OXALOSUCCINATE DECARBOXYLASE, IDH; COMPND 5 EC: 1.1.1.42; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: ICD; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: JLK1; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PUC; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTK513; SOURCE 11 EXPRESSION_SYSTEM_GENE: ICD KEYWDS OXIDOREDUCTASE, OXIDOREDUCTASE (NAD(A)-CHOH(D)), NADP, KEYWDS 2 PHOSPHORYLATION, GLYOXYLATE BYPASS EXPDTA X-RAY DIFFRACTION AUTHOR S.A.DOYLE,P.T.BEERNINK,D.E.KOSHLAND JUNIOR REVDAT 4 01-MAY-24 1HJ6 1 LINK REVDAT 3 24-FEB-09 1HJ6 1 VERSN REVDAT 2 31-MAY-01 1HJ6 1 JRNL REVDAT 1 16-JAN-01 1HJ6 0 JRNL AUTH S.A.DOYLE,P.T.BEERNINK,D.E.KOSHLAND JUNIOR JRNL TITL STRUCTURAL BASIS FOR A CHANGE IN SUBSTRATE SPECIFICITY: JRNL TITL 2 CRYSTAL STRUCTURE OF S113E ISOCITRATE DEHYDROGENASE IN A JRNL TITL 3 COMPLEX WITH ISOPROPYLMALATE, MG2+ AND NADP JRNL REF BIOCHEMISTRY V. 40 4234 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11284679 JRNL DOI 10.1021/BI002533Q REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 56218 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) : 0.206 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5332 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5714 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 632 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 : 3199 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 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 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HJ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1290005699. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.30 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 265721 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 21.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.70900 REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: IDH-ISOPROPYLMALATE COMPLEX STRUCTURE (A. MESECAR, REMARK 200 D.E. KOSHLAND, UNPUBLISHED DATA) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 34-44% (NH4)2SO4, 35MM NA2HPO4, 9 MM REMARK 280 CITRIC ACID, 100 MM NACL, 0.2 MM DTT, PH 5.4, PH 7.30 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 75.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.15000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.87500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.15000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.62500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.15000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.87500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.15000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.62500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.25000 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 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 CHAIN A CONTAINS ENGINEERED MUTATION S113E 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 1 REMARK 465 GLU A 2 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 CB GLU A 371 O HOH A 2211 1.02 REMARK 500 O3D NAP A 1420 O HOH A 2228 1.31 REMARK 500 CB GLN A 80 O HOH A 2059 1.32 REMARK 500 O THR A 105 O HOH A 2074 1.39 REMARK 500 CA PRO A 106 O HOH A 2074 1.43 REMARK 500 CG GLN A 80 O HOH A 2059 1.52 REMARK 500 N PRO A 106 O HOH A 2074 1.55 REMARK 500 C THR A 105 O HOH A 2074 1.56 REMARK 500 N ASN A 415 O HOH A 2223 1.62 REMARK 500 ND2 ASN A 415 O HOH A 2223 1.63 REMARK 500 CA GLU A 371 O HOH A 2211 1.72 REMARK 500 CD GLN A 80 O HOH A 2059 1.73 REMARK 500 N MET A 416 O HOH A 2224 1.78 REMARK 500 C PRO A 106 O HOH A 2074 1.83 REMARK 500 CA GLY A 59 O HOH A 2033 1.86 REMARK 500 O GLY A 109 O HOH A 2077 1.86 REMARK 500 NE2 GLN A 80 O HOH A 2059 1.88 REMARK 500 O MET A 416 O HOH A 2224 1.88 REMARK 500 N ASN A 232 O HOH A 2152 1.92 REMARK 500 CA GLY A 109 O HOH A 2077 1.93 REMARK 500 N GLY A 59 O HOH A 2033 1.93 REMARK 500 CG ASN A 415 O HOH A 2223 1.95 REMARK 500 OE1 GLN A 80 O HOH A 2058 1.96 REMARK 500 CG GLN A 80 O HOH A 2056 2.00 REMARK 500 C GLY A 231 O HOH A 2152 2.01 REMARK 500 C GLU A 414 O HOH A 2223 2.09 REMARK 500 N GLU A 371 O HOH A 2211 2.10 REMARK 500 CA ASN A 415 O HOH A 2223 2.10 REMARK 500 CG GLU A 371 O HOH A 2211 2.10 REMARK 500 C GLY A 109 O HOH A 2077 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 N GLY A 109 OE2 GLU A 371 4535 0.62 REMARK 500 NH2 ARG A 250 C GLU A 414 5354 0.75 REMARK 500 C ALA A 56 CB VAL A 107 3344 0.80 REMARK 500 CA GLY A 109 OE2 GLU A 371 4535 0.95 REMARK 500 N GLY A 109 CD GLU A 371 4535 0.97 REMARK 500 O ALA A 56 CB VAL A 107 3344 0.98 REMARK 500 NH2 ARG A 250 CA GLU A 414 5354 1.14 REMARK 500 CZ ARG A 250 CA GLU A 414 5354 1.14 REMARK 500 N TYR A 57 CG2 VAL A 107 3344 1.18 REMARK 500 C ALA A 56 CG2 VAL A 107 3344 1.28 REMARK 500 CA ALA A 56 CG1 VAL A 107 3344 1.32 REMARK 500 C ALA A 56 CG1 VAL A 107 3344 1.35 REMARK 500 NE ARG A 250 CA GLU A 414 5354 1.42 REMARK 500 NH2 ARG A 250 O GLU A 414 5354 1.43 REMARK 500 O ALA A 56 CG1 VAL A 107 3344 1.44 REMARK 500 O ALA A 56 CA VAL A 107 3344 1.50 REMARK 500 OE1 GLU A 60 CG2 THR A 104 3344 1.53 REMARK 500 NE ARG A 250 CG GLU A 414 5354 1.56 REMARK 500 N TYR A 57 CB VAL A 107 3344 1.58 REMARK 500 CA TYR A 57 CG2 VAL A 107 3344 1.59 REMARK 500 NE ARG A 250 CB GLU A 414 5354 1.60 REMARK 500 O ALA A 56 CG2 VAL A 107 3344 1.61 REMARK 500 CE1 TYR A 57 O VAL A 107 3344 1.61 REMARK 500 CB ARG A 250 CG GLU A 414 5354 1.70 REMARK 500 CA GLY A 108 CG GLU A 371 4535 1.72 REMARK 500 CD ARG A 250 CG GLU A 414 5354 1.85 REMARK 500 C GLY A 108 CD GLU A 371 4535 1.87 REMARK 500 C GLY A 108 OE2 GLU A 371 4535 1.87 REMARK 500 OE1 GLU A 25 OE1 GLU A 72 3344 1.88 REMARK 500 N GLY A 109 CG GLU A 371 4535 1.90 REMARK 500 CB ARG A 250 CD GLU A 414 5354 1.91 REMARK 500 NH2 ARG A 250 N ASN A 415 5354 1.94 REMARK 500 CA GLY A 109 CD GLU A 371 4535 2.00 REMARK 500 OE2 GLU A 60 OG1 THR A 104 3344 2.02 REMARK 500 C GLY A 109 OE2 GLU A 371 4535 2.02 REMARK 500 CZ ARG A 250 C GLU A 414 5354 2.04 REMARK 500 CD1 TYR A 57 N VAL A 107 3344 2.07 REMARK 500 N GLY A 109 OE1 GLU A 371 4535 2.07 REMARK 500 NZ LYS A 55 OD2 ASP A 243 5344 2.07 REMARK 500 CD GLU A 60 CG2 THR A 104 3344 2.09 REMARK 500 C GLY A 108 CG GLU A 371 4535 2.11 REMARK 500 CG ARG A 250 CG GLU A 414 5354 2.11 REMARK 500 CA ALA A 56 CB VAL A 107 3344 2.11 REMARK 500 CD GLU A 60 OG1 THR A 104 3344 2.11 REMARK 500 CZ ARG A 250 N GLU A 414 5354 2.12 REMARK 500 O HOH A 2032 O HOH A 2152 5344 2.15 REMARK 500 CD GLU A 25 OE1 GLU A 72 3344 2.16 REMARK 500 CB ALA A 56 CG1 VAL A 107 3344 2.16 REMARK 500 CE LYS A 55 OD1 ASP A 243 5344 2.16 REMARK 500 CD1 TYR A 57 O VAL A 107 3344 2.17 REMARK 500 REMARK 500 THIS ENTRY HAS 51 SYMMETRY CONTACTS 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 LYS A 58 45.32 33.75 REMARK 500 ASP A 81 -19.66 84.36 REMARK 500 ARG A 96 -35.27 63.02 REMARK 500 ASP A 148 83.84 -150.58 REMARK 500 GLU A 157 -140.52 -130.16 REMARK 500 ASP A 158 -164.23 67.03 REMARK 500 ASP A 168 -1.58 72.15 REMARK 500 MET A 234 77.09 -109.15 REMARK 500 THR A 237 -72.08 -124.82 REMARK 500 ASP A 259 -140.00 60.15 REMARK 500 ARG A 292 53.97 -143.73 REMARK 500 ASP A 297 -95.88 -130.43 REMARK 500 ALA A 342 72.05 22.39 REMARK 500 ALA A 346 143.24 -39.68 REMARK 500 TRP A 369 57.76 -91.25 REMARK 500 LEU A 396 35.73 76.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1421 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD2 REMARK 620 2 ASP A 307 OD1 95.5 REMARK 620 3 IPM A1419 O1 84.6 87.5 REMARK 620 4 IPM A1419 O3 157.1 84.1 72.6 REMARK 620 5 HOH A2187 O 112.3 78.7 158.9 90.1 REMARK 620 6 HOH A2201 O 89.4 175.2 93.1 91.5 99.4 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A1421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IPM A1419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A1420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A1418 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AI2 RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND REMARK 900 CALCIUM (FLASH-COOLED) REMARK 900 RELATED ID: 1AI3 RELATED DB: PDB REMARK 900 ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL REMARK 900 STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES REMARK 900 RELATED ID: 1BL5 RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE REMARK 900 STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION REMARK 900 RELATED ID: 1CW1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO REMARK 900 ISOCITRATE AND MN2+ REMARK 900 RELATED ID: 1CW4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH REMARK 900 ALPHA- KETOGLUTARATE REMARK 900 RELATED ID: 1CW7 RELATED DB: PDB REMARK 900 LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG- REMARK 900 ISOCITRATE REMARK 900 RELATED ID: 1GRO RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: ISOCITRATE DEHYDROGENASE; CHAIN: NULL; EC: REMARK 900 1.1.1.42; ENGINEERED: YES; MUTATION: S113E, N115L REMARK 900 RELATED ID: 1GRP RELATED DB: PDB REMARK 900 MOL_ID: 1; MOLECULE: ISOCITRATE DEHYDROGENASE; CHAIN: NULL; EC: REMARK 900 1.1.1.42; MUTATION: N115L REMARK 900 RELATED ID: 1IDC RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE REMARK 900 INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1IDD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME REMARK 900 RELATED ID: 1IDE RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE REMARK 900 COMPLEX (LAUE DETERMINATION) REMARK 900 RELATED ID: 1IDF RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME REMARK 900 RELATED ID: 1ISO RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP+ --> NAD+ REMARK 900 SPECIFICITY-REVERSAL MUTANT REMARK 900 RELATED ID: 1SJS RELATED DB: PDB REMARK 900 ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY REMARK 900 DOMAIN SHIFTING REMARK 999 REMARK 999 SEQUENCE REMARK 999 SER 113 TO GLU MUTANT ENZYME DBREF 1HJ6 A 1 416 UNP P08200 IDH_ECOLI 1 416 SEQRES 1 A 416 MET GLU SER LYS VAL VAL VAL PRO ALA GLN GLY LYS LYS SEQRES 2 A 416 ILE THR LEU GLN ASN GLY LYS LEU ASN VAL PRO GLU ASN SEQRES 3 A 416 PRO ILE ILE PRO TYR ILE GLU GLY ASP GLY ILE GLY VAL SEQRES 4 A 416 ASP VAL THR PRO ALA MET LEU LYS VAL VAL ASP ALA ALA SEQRES 5 A 416 VAL GLU LYS ALA TYR LYS GLY GLU ARG LYS ILE SER TRP SEQRES 6 A 416 MET GLU ILE TYR THR GLY GLU LYS SER THR GLN VAL TYR SEQRES 7 A 416 GLY GLN ASP VAL TRP LEU PRO ALA GLU THR LEU ASP LEU SEQRES 8 A 416 ILE ARG GLU TYR ARG VAL ALA ILE LYS GLY PRO LEU THR SEQRES 9 A 416 THR PRO VAL GLY GLY GLY ILE ARG GLU LEU ASN VAL ALA SEQRES 10 A 416 LEU ARG GLN GLU LEU ASP LEU TYR ILE CYS LEU ARG PRO SEQRES 11 A 416 VAL ARG TYR TYR GLN GLY THR PRO SER PRO VAL LYS HIS SEQRES 12 A 416 PRO GLU LEU THR ASP MET VAL ILE PHE ARG GLU ASN SER SEQRES 13 A 416 GLU ASP ILE TYR ALA GLY ILE GLU TRP LYS ALA ASP SER SEQRES 14 A 416 ALA ASP ALA GLU LYS VAL ILE LYS PHE LEU ARG GLU GLU SEQRES 15 A 416 MET GLY VAL LYS LYS ILE ARG PHE PRO GLU HIS CYS GLY SEQRES 16 A 416 ILE GLY ILE LYS PRO CYS SER GLU GLU GLY THR LYS ARG SEQRES 17 A 416 LEU VAL ARG ALA ALA ILE GLU TYR ALA ILE ALA ASN ASP SEQRES 18 A 416 ARG ASP SER VAL THR LEU VAL HIS LYS GLY ASN ILE MET SEQRES 19 A 416 LYS PHE THR GLU GLY ALA PHE LYS ASP TRP GLY TYR GLN SEQRES 20 A 416 LEU ALA ARG GLU GLU PHE GLY GLY GLU LEU ILE ASP GLY SEQRES 21 A 416 GLY PRO TRP LEU LYS VAL LYS ASN PRO ASN THR GLY LYS SEQRES 22 A 416 GLU ILE VAL ILE LYS ASP VAL ILE ALA ASP ALA PHE LEU SEQRES 23 A 416 GLN GLN ILE LEU LEU ARG PRO ALA GLU TYR ASP VAL ILE SEQRES 24 A 416 ALA CYS MET ASN LEU ASN GLY ASP TYR ILE SER ASP ALA SEQRES 25 A 416 LEU ALA ALA GLN VAL GLY GLY ILE GLY ILE ALA PRO GLY SEQRES 26 A 416 ALA ASN ILE GLY ASP GLU CYS ALA LEU PHE GLU ALA THR SEQRES 27 A 416 HIS GLY THR ALA PRO LYS TYR ALA GLY GLN ASP LYS VAL SEQRES 28 A 416 ASN PRO GLY SER ILE ILE LEU SER ALA GLU MET MET LEU SEQRES 29 A 416 ARG HIS MET GLY TRP THR GLU ALA ALA ASP LEU ILE VAL SEQRES 30 A 416 LYS GLY MET GLU GLY ALA ILE ASN ALA LYS THR VAL THR SEQRES 31 A 416 TYR ASP PHE GLU ARG LEU MET ASP GLY ALA LYS LEU LEU SEQRES 32 A 416 LYS CYS SER GLU PHE GLY ASP ALA ILE ILE GLU ASN MET HET GOL A1417 6 HET GOL A1418 6 HET IPM A1419 12 HET NAP A1420 48 HET MG A1421 1 HETNAM GOL GLYCEROL HETNAM IPM 3-ISOPROPYLMALIC ACID HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 IPM C7 H12 O5 FORMUL 5 NAP C21 H28 N7 O17 P3 FORMUL 6 MG MG 2+ FORMUL 7 HOH *232(H2 O) HELIX 1 1 ILE A 37 TYR A 57 1 21 HELIX 2 2 GLY A 71 GLY A 79 1 9 HELIX 3 3 PRO A 85 ARG A 96 1 12 HELIX 4 4 GLU A 113 LEU A 122 1 10 HELIX 5 5 HIS A 143 LEU A 146 5 4 HELIX 6 6 GLU A 157 GLY A 162 5 6 HELIX 7 7 SER A 169 GLU A 182 1 14 HELIX 8 8 SER A 202 ASN A 220 1 19 HELIX 9 9 THR A 237 GLY A 254 1 18 HELIX 10 10 ALA A 282 ARG A 292 1 11 HELIX 11 11 PRO A 293 TYR A 296 5 4 HELIX 12 12 MET A 302 ALA A 315 1 14 HELIX 13 13 GLN A 316 GLY A 318 5 3 HELIX 14 14 GLY A 319 ALA A 323 5 5 HELIX 15 15 PRO A 353 GLY A 368 1 16 HELIX 16 16 TRP A 369 ALA A 386 1 18 HELIX 17 17 THR A 390 ARG A 395 1 6 HELIX 18 18 LYS A 404 ASN A 415 1 12 SHEET 1 A 2 THR A 15 GLN A 17 0 SHEET 2 A 2 LYS A 20 ASN A 22 -1 N ASN A 22 O THR A 15 SHEET 1 B11 SER A 64 GLU A 67 0 SHEET 2 B11 ILE A 28 ILE A 32 1 N ILE A 29 O SER A 64 SHEET 3 B11 VAL A 97 LYS A 100 1 N ILE A 99 O PRO A 30 SHEET 4 B11 ALA A 333 GLU A 336 1 N ALA A 333 O ALA A 98 SHEET 5 B11 ALA A 326 ILE A 328 -1 N ASN A 327 O LEU A 334 SHEET 6 B11 ILE A 126 ARG A 132 -1 N LEU A 128 O ALA A 326 SHEET 7 B11 ASP A 148 GLU A 154 -1 N ARG A 153 O CYS A 127 SHEET 8 B11 VAL A 298 CYS A 301 1 N ILE A 299 O VAL A 150 SHEET 9 B11 SER A 224 HIS A 229 1 N THR A 226 O VAL A 298 SHEET 10 B11 GLU A 274 ILE A 281 1 N VAL A 276 O VAL A 225 SHEET 11 B11 LEU A 264 LYS A 267 -1 N VAL A 266 O ILE A 275 LINK OD2 ASP A 283 MG MG A1421 7555 1555 2.27 LINK OD1 ASP A 307 MG MG A1421 1555 1555 2.17 LINK O1 IPM A1419 MG MG A1421 1555 1555 2.37 LINK O3 IPM A1419 MG MG A1421 1555 1555 2.30 LINK MG MG A1421 O HOH A2187 1555 1555 2.19 LINK MG MG A1421 O HOH A2201 1555 1555 2.19 CISPEP 1 GLY A 261 PRO A 262 0 0.12 SITE 1 AC1 5 ASP A 283 ASP A 307 IPM A1419 HOH A2187 SITE 2 AC1 5 HOH A2201 SITE 1 AC2 12 GLU A 113 ARG A 119 ARG A 129 ARG A 153 SITE 2 AC2 12 TYR A 160 LYS A 230 ILE A 233 ASP A 283 SITE 3 AC2 12 ASP A 307 NAP A1420 MG A1421 HOH A2226 SITE 1 AC3 26 GLU A 60 LYS A 100 PRO A 102 LEU A 103 SITE 2 AC3 26 THR A 104 ASN A 115 GLN A 288 ARG A 292 SITE 3 AC3 26 ILE A 320 GLY A 321 GLU A 336 THR A 338 SITE 4 AC3 26 HIS A 339 GLY A 340 THR A 341 ALA A 342 SITE 5 AC3 26 TYR A 345 VAL A 351 ASN A 352 TYR A 391 SITE 6 AC3 26 ASP A 392 IPM A1419 HOH A2227 HOH A2228 SITE 7 AC3 26 HOH A2230 HOH A2232 SITE 1 AC4 8 ARG A 96 ILE A 328 GLY A 329 ASP A 330 SITE 2 AC4 8 CYS A 332 ALA A 333 HIS A 366 GOL A1418 SITE 1 AC5 5 PHE A 152 HIS A 366 GOL A1417 HOH A2142 SITE 2 AC5 5 HOH A2206 CRYST1 102.300 102.300 150.500 90.00 90.00 90.00 P 43 21 2 8 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 0.009775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006644 0.00000