PDB Short entry for 1IDC HEADER OXIDOREDUCTASE (NAD(A)-CHOH(D)) 18-JAN-95 1IDC TITLE ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE TITLE 2 INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IDH; COMPND 5 EC: 1.1.1.42; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: RATE-LIMITED ENOLATE INTERMEDIATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: JLK1; SOURCE 5 VARIANT: ICD(-) (DEFICIENT IN WT IDH GENE); SOURCE 6 GENE: ICD; SOURCE 7 EXPRESSION_SYSTEM: PEMBL (DENTE ET AL 1983 NUC ACIDS RES 11,1645); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: BACTERIAL; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTK513; SOURCE 10 EXPRESSION_SYSTEM_GENE: ICD KEYWDS OXIDOREDUCTASE (NAD(A)-CHOH(D)) EXPDTA X-RAY DIFFRACTION AUTHOR J.M.BOLDUC,D.H.DYER,W.G.SCOTT,P.SINGER,R.M.SWEET,D.E.KOSHLAND JUNIOR, AUTHOR 2 B.L.STODDARD REVDAT 6 03-NOV-21 1IDC 1 REMARK SEQADV LINK REVDAT 5 29-NOV-17 1IDC 1 REMARK HELIX REVDAT 4 13-JUL-11 1IDC 1 VERSN REVDAT 3 24-FEB-09 1IDC 1 VERSN REVDAT 2 01-APR-03 1IDC 1 JRNL REVDAT 1 08-MAR-96 1IDC 0 JRNL AUTH J.M.BOLDUC,D.H.DYER,W.G.SCOTT,P.SINGER,R.M.SWEET, JRNL AUTH 2 D.E.KOSHLAND JR.,B.L.STODDARD JRNL TITL MUTAGENESIS AND LAUE STRUCTURES OF ENZYME INTERMEDIATES: JRNL TITL 2 ISOCITRATE DEHYDROGENASE. JRNL REF SCIENCE V. 268 1312 1995 JRNL REFN ISSN 0036-8075 JRNL PMID 7761851 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.H.HURLEY,A.M.DEAN,D.E.KOSHLAND JUNIOR,R.M.STROUD REMARK 1 TITL CATALYTIC MECHANISM OF NADP+-DEPENDENT ISOCITRATE REMARK 1 TITL 2 DEHYDROGENASE: IMPLICATIONS FROM THE STRUCTURES OF REMARK 1 TITL 3 MAGNESIUM-ISOCITRATE AND NADP+ COMPLEXES REMARK 1 REF BIOCHEMISTRY V. 30 8671 1991 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.H.HURLEY,A.M.DEAN,P.E.THORSNESS,D.E.KOSHLAND JUNIOR, REMARK 1 AUTH 2 R.M.STROUD REMARK 1 TITL REGULATION OF ISOCITRATE DEHYDROGENASE BY PHOSPHORYLATION REMARK 1 TITL 2 INVOLVES NO LONG-RANGE CONFORMATIONAL CHANGE IN THE FREE REMARK 1 TITL 3 ENZYME REMARK 1 REF J.BIOL.CHEM. V. 265 3599 1990 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.H.HURLEY,A.M.DEAN,J.L.SOHL,D.E.KOSHLAND JUNIOR,R.M.STROUD REMARK 1 TITL REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE REMARK 1 TITL 2 SITE REMARK 1 REF SCIENCE V. 249 1012 1990 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 4 REMARK 1 AUTH J.H.HURLEY,P.E.THORSNESS,V.RAMALINGAM,N.H.HELMERS, REMARK 1 AUTH 2 D.E.KOSHLAND JUNIOR,R.M.STROUD REMARK 1 TITL STRUCTURE OF A BACTERIAL ENZYME REGULATED BY REMARK 1 TITL 2 PHOSPHORYLATION, ISOCITRATE DEHYDROGENASE REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 86 8635 1989 REMARK 1 REFN ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 17316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : DATA COLLECTED FROM FOUR REMARK 3 SEPARATE CRYSTALS AT X26-C REMARK 3 (POLYCHROMATIC LAUE BEAM LINE REMARK 3 AT BROOKHAVEN NATIONAL REMARK 3 LABORATORY) AND MERGED REMARK 3 TOGETHER WITH LAUENORM IN REMARK 3 OXFORD LAUE DATA REDUCTION REMARK 3 PACKAGE. REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 3195 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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) : 0.018 REMARK 3 BOND ANGLES (DEGREES) : 3.661 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.07 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.839 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IDC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174108. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-93 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : L REMARK 200 WAVELENGTH OR RANGE (A) : 0.7 - 2.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : OXFORD LAUE PACKAGE (J.CAMPBELL) REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17316 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 62.0 REMARK 200 DATA REDUNDANCY : 18.70 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: LAUE REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 75.15000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.55000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.72500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.55000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.57500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.55000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.72500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.55000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.55000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.57500 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 75.15000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 7860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 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 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 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN A 10 CG CD OE1 NE2 REMARK 480 GLN A 17 CG CD OE1 NE2 REMARK 480 ASN A 18 CG OD1 ND2 REMARK 480 LYS A 20 CG CD CE NZ REMARK 480 LYS A 186 CG CD CE NZ REMARK 480 GLU A 192 CD OE1 OE2 REMARK 480 LYS A 273 CG CD CE NZ REMARK 480 LYS A 344 CG CD CE NZ 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 OH TYR A 160 C1 OXS A 418 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 143 NE2 HIS A 143 CD2 -0.073 REMARK 500 HIS A 193 NE2 HIS A 193 CD2 -0.076 REMARK 500 HIS A 229 NE2 HIS A 229 CD2 -0.079 REMARK 500 HIS A 366 NE2 HIS A 366 CD2 -0.069 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 TYR A 57 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 TRP A 65 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 TRP A 65 CG - CD2 - CE3 ANGL. DEV. = 6.2 DEGREES REMARK 500 TYR A 69 CA - C - N ANGL. DEV. = -14.0 DEGREES REMARK 500 TYR A 69 O - C - N ANGL. DEV. = 9.8 DEGREES REMARK 500 TRP A 83 CD1 - CG - CD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 TRP A 83 CB - CG - CD1 ANGL. DEV. = -8.1 DEGREES REMARK 500 TRP A 83 CG - CD1 - NE1 ANGL. DEV. = -6.1 DEGREES REMARK 500 TRP A 83 CE2 - CD2 - CG ANGL. DEV. = -6.6 DEGREES REMARK 500 TRP A 83 CG - CD2 - CE3 ANGL. DEV. = 5.8 DEGREES REMARK 500 TYR A 95 CA - CB - CG ANGL. DEV. = -11.4 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 VAL A 141 N - CA - CB ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 TRP A 165 CD1 - CG - CD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 TRP A 165 CE2 - CD2 - CG ANGL. DEV. = -6.3 DEGREES REMARK 500 CYS A 194 CA - CB - SG ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 MET A 230 CG - SD - CE ANGL. DEV. = 12.2 DEGREES REMARK 500 TRP A 244 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP A 244 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES REMARK 500 TRP A 244 CG - CD2 - CE3 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 250 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 259 CA - C - N ANGL. DEV. = 12.6 DEGREES REMARK 500 LEU A 286 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 ILE A 299 CG1 - CB - CG2 ANGL. DEV. = -13.7 DEGREES REMARK 500 TRP A 369 CD1 - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP A 369 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 VAL A 389 CB - CA - C ANGL. DEV. = 11.7 DEGREES REMARK 500 VAL A 389 N - CA - CB ANGL. DEV. = -19.2 DEGREES REMARK 500 VAL A 389 CG1 - CB - CG2 ANGL. DEV. = 12.0 DEGREES REMARK 500 ARG A 395 NE - CZ - NH1 ANGL. DEV. = 3.3 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 ASN A 18 73.13 23.34 REMARK 500 LYS A 55 -71.27 -64.32 REMARK 500 TYR A 78 -65.86 -95.38 REMARK 500 GLN A 80 4.12 -69.35 REMARK 500 ARG A 96 -36.10 71.54 REMARK 500 VAL A 131 103.08 -167.77 REMARK 500 PHE A 152 77.18 -114.23 REMARK 500 ASP A 158 170.12 71.35 REMARK 500 GLU A 181 -76.73 -77.41 REMARK 500 MET A 230 54.23 -100.27 REMARK 500 ILE A 233 -50.99 -126.15 REMARK 500 THR A 237 -89.88 -118.52 REMARK 500 ASP A 259 -82.91 42.81 REMARK 500 ALA A 282 -56.95 -26.73 REMARK 500 ASP A 297 -94.92 -140.84 REMARK 500 VAL A 389 -166.96 -128.52 REMARK 500 TYR A 391 -31.90 -39.41 REMARK 500 ARG A 395 -16.95 -49.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 95 0.07 SIDE CHAIN REMARK 500 TYR A 296 0.07 SIDE CHAIN REMARK 500 TYR A 345 0.09 SIDE CHAIN 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 A 417 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD2 REMARK 620 2 ASP A 307 OD1 86.1 REMARK 620 3 ASP A 311 OD2 74.3 115.1 REMARK 620 4 OXS A 418 O7 147.5 88.4 136.1 REMARK 620 5 OXS A 418 O5 83.7 119.2 119.0 71.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: SUB REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ISOCITRATE/MG++ BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXS A 418 DBREF 1IDC A 1 416 UNP P08200 IDH_ECOLI 1 416 SEQADV 1IDC MET A 230 UNP P08200 LYS 230 ENGINEERED MUTATION 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 SER 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 MET 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 MG A 417 1 HET OXS A 418 13 HETNAM MG MAGNESIUM ION HETNAM OXS 2-OXALOSUCCINIC ACID FORMUL 2 MG MG 2+ FORMUL 3 OXS C6 H6 O7 HELIX 1 HA ILE A 37 LYS A 58 1 22 HELIX 2 HB THR A 70 TYR A 78 1 9 HELIX 3 HC PRO A 85 TYR A 95 1 11 HELIX 4 HD SER A 113 LEU A 124 1 12 HELIX 5 HE ASP A 168 MET A 183 1 16 HELIX 6 HF GLU A 203 ARG A 222 1 20 HELIX 7 HG LYS A 235 PHE A 253 1 19 HELIX 8 HH ILE A 281 LEU A 291 1 11 HELIX 9 HI ASN A 303 VAL A 317 1 15 HELIX 10 HJ PRO A 353 MET A 367 1 15 HELIX 11 HK TRP A 369 THR A 388 1 20 HELIX 12 HL THR A 390 MET A 397 1 8 HELIX 13 HM LYS A 404 ASN A 415 1 12 SHEET 1 S112 ARG A 61 ILE A 68 0 SHEET 2 S112 GLU A 25 ILE A 32 1 SHEET 3 S112 ARG A 96 LYS A 100 1 SHEET 4 S112 ALA A 333 GLU A 336 1 SHEET 5 S112 GLY A 325 ILE A 328 -1 SHEET 6 S112 TYR A 125 ARG A 132 -1 SHEET 7 S112 THR A 147 ARG A 153 -1 SHEET 8 S112 ASP A 297 MET A 302 1 SHEET 9 S112 SER A 224 HIS A 229 1 SHEET 10 S112 LYS A 273 VAL A 280 1 SHEET 11 S112 LEU A 264 LYS A 267 -1 SHEET 12 S112 GLY A 254 GLU A 256 -1 SHEET 1 S2 2 ILE A 163 ALA A 167 0 SHEET 2 S2 2 HIS A 193 SER A 202 -1 LINK OH TYR A 160 O1 OXS A 418 1555 1555 1.71 LINK OD2 ASP A 283 MG MG A 417 7555 1555 2.20 LINK OD1 ASP A 307 MG MG A 417 1555 1555 2.01 LINK OD2 ASP A 311 MG MG A 417 1555 1555 3.05 LINK MG MG A 417 O7 OXS A 418 1555 1555 2.46 LINK MG MG A 417 O5 OXS A 418 1555 1555 2.25 CISPEP 1 GLY A 261 PRO A 262 0 9.72 SITE 1 SUB 8 SER A 113 ASN A 115 ARG A 119 ARG A 129 SITE 2 SUB 8 ARG A 153 TYR A 160 ASP A 307 ASP A 311 SITE 1 AC1 4 ASP A 283 ASP A 307 ASP A 311 OXS A 418 SITE 1 AC2 10 SER A 113 ASN A 115 VAL A 116 ARG A 119 SITE 2 AC2 10 ARG A 153 TYR A 160 ILE A 233 ASP A 283 SITE 3 AC2 10 ASP A 307 MG A 417 CRYST1 105.100 105.100 150.300 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 0.009515 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006653 0.00000