HEADER OXIDOREDUCTASE(NAD(A)-CHOH(D)) 15-JUN-93 1IKA TITLE STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 TITLE 2 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY TITLE 3 DECARBOXYLATION OF ISOCITRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.42; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS OXIDOREDUCTASE(NAD(A)-CHOH(D)) EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STODDARD,D.E.KOSHLAND JUNIOR REVDAT 7 07-FEB-24 1IKA 1 REMARK LINK REVDAT 6 14-AUG-19 1IKA 1 REMARK REVDAT 5 17-JUL-19 1IKA 1 REMARK REVDAT 4 13-JUL-11 1IKA 1 VERSN REVDAT 3 24-FEB-09 1IKA 1 VERSN REVDAT 2 01-APR-03 1IKA 1 JRNL REVDAT 1 31-JUL-94 1IKA 0 JRNL AUTH B.L.STODDARD,D.E.KOSHLAND JR. JRNL TITL STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH JRNL TITL 2 ALPHA-KETOGLUTARATE AT 2.7-A RESOLUTION: CONFORMATIONAL JRNL TITL 3 CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE. JRNL REF BIOCHEMISTRY V. 32 9317 1993 JRNL REFN ISSN 0006-2960 JRNL PMID 8369301 JRNL DOI 10.1021/BI00087A009 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.L.STODDARD,A.DEAN,D.E.KOSHLAND JUNIOR REMARK 1 TITL THE STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ISOCITRATE, REMARK 1 TITL 2 NADP, AND CALCIUM AT 2.5 ANGSTROMS RESOLUTION: A REMARK 1 TITL 3 PSEUDO-MICHAELIS TERNARY COMPLEX REMARK 1 REF BIOCHEMISTRY V. 32 9310 1993 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 14729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3196 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 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 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IKA 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_1000174170. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 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: 7920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 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 N CA C O CB CG CD REMARK 480 GLN A 10 OE1 NE2 REMARK 480 GLN A 17 N CA C O CB CG CD REMARK 480 GLN A 17 OE1 NE2 REMARK 480 ASN A 18 N CA C O CB CG OD1 REMARK 480 ASN A 18 ND2 REMARK 480 LYS A 20 N CA C O CB CG CD REMARK 480 LYS A 20 CE NZ REMARK 480 ASP A 81 N CA C O CB CG OD1 REMARK 480 ASP A 81 OD2 REMARK 480 GLU A 182 N CA C O CB CG CD REMARK 480 GLU A 182 OE1 OE2 REMARK 480 LYS A 186 N CA C O CB CG CD REMARK 480 LYS A 186 CE NZ REMARK 480 GLU A 204 N CA C O CB CG CD REMARK 480 GLU A 204 OE1 OE2 REMARK 480 ASP A 259 N CA C O CB CG OD1 REMARK 480 ASP A 259 OD2 REMARK 480 LYS A 273 N CA C O CB CG CD REMARK 480 LYS A 273 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 OD1 ASP A 307 O2 AKG A 418 2.08 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 VAL A 23 CA VAL A 23 CB 0.145 REMARK 500 VAL A 97 CA VAL A 97 CB 0.132 REMARK 500 ARG A 119 CZ ARG A 119 NH2 0.080 REMARK 500 HIS A 143 NE2 HIS A 143 CD2 -0.070 REMARK 500 VAL A 150 CA VAL A 150 CB 0.178 REMARK 500 HIS A 229 NE2 HIS A 229 CD2 -0.096 REMARK 500 TRP A 244 CG TRP A 244 CD2 -0.103 REMARK 500 HIS A 339 NE2 HIS A 339 CD2 -0.082 REMARK 500 HIS A 366 NE2 HIS A 366 CD2 -0.077 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 VAL A 5 CA - C - N ANGL. DEV. = -15.6 DEGREES REMARK 500 PRO A 8 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 PRO A 8 N - CA - C ANGL. DEV. = 20.4 DEGREES REMARK 500 ALA A 9 N - CA - C ANGL. DEV. = 16.8 DEGREES REMARK 500 ILE A 28 CA - C - N ANGL. DEV. = -17.2 DEGREES REMARK 500 ILE A 28 O - C - N ANGL. DEV. = 11.5 DEGREES REMARK 500 TYR A 31 CB - CG - CD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 GLU A 33 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 VAL A 49 CG1 - CB - CG2 ANGL. DEV. = -10.6 DEGREES REMARK 500 TYR A 57 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 TRP A 65 CD1 - CG - CD2 ANGL. DEV. = 7.8 DEGREES REMARK 500 TRP A 65 CE2 - CD2 - CG ANGL. DEV. = -6.3 DEGREES REMARK 500 TYR A 69 CB - CA - C ANGL. DEV. = -15.5 DEGREES REMARK 500 TYR A 69 CB - CG - CD1 ANGL. DEV. = -4.1 DEGREES REMARK 500 VAL A 77 CG1 - CB - CG2 ANGL. DEV. = -14.8 DEGREES REMARK 500 VAL A 82 CA - CB - CG1 ANGL. DEV. = -9.4 DEGREES REMARK 500 TRP A 83 CD1 - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 TRP A 83 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 LEU A 84 CA - CB - CG ANGL. DEV. = 14.2 DEGREES REMARK 500 PRO A 85 CA - C - N ANGL. DEV. = -18.1 DEGREES REMARK 500 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 VAL A 97 CA - CB - CG1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 112 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 119 CG - CD - NE ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR A 125 CA - CB - CG ANGL. DEV. = 19.5 DEGREES REMARK 500 LEU A 128 CA - CB - CG ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 129 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 TYR A 133 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 TYR A 134 CB - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 TYR A 160 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ILE A 163 N - CA - C ANGL. DEV. = -23.2 DEGREES REMARK 500 TRP A 165 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 VAL A 185 CA - C - N ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG A 189 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 CYS A 194 CA - CB - SG ANGL. DEV. = 12.6 DEGREES REMARK 500 CYS A 201 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 VAL A 210 CG1 - CB - CG2 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG A 211 CA - CB - CG ANGL. DEV. = 15.1 DEGREES REMARK 500 ILE A 214 CA - C - N ANGL. DEV. = 18.5 DEGREES REMARK 500 ILE A 214 O - C - N ANGL. DEV. = -9.7 DEGREES REMARK 500 TYR A 216 CB - CG - CD2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 5.3 DEGREES REMARK 500 LEU A 227 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 GLY A 231 CA - C - N ANGL. DEV. = -14.2 DEGREES REMARK 500 GLY A 231 O - C - N ANGL. DEV. = 14.4 DEGREES REMARK 500 PHE A 236 O - C - N ANGL. DEV. = -10.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 97 ANGLE DEVIATIONS. 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 4 -147.53 79.69 REMARK 500 VAL A 5 93.24 25.21 REMARK 500 PRO A 8 48.93 -59.55 REMARK 500 ALA A 9 -64.85 36.79 REMARK 500 GLN A 17 -159.38 -157.69 REMARK 500 ASN A 18 74.85 -67.25 REMARK 500 LYS A 20 91.51 -51.15 REMARK 500 ASN A 26 65.44 -116.23 REMARK 500 LYS A 73 17.49 -68.41 REMARK 500 THR A 75 -63.42 -128.34 REMARK 500 VAL A 77 -20.13 -171.25 REMARK 500 TYR A 78 -71.71 -142.38 REMARK 500 VAL A 82 58.20 -104.88 REMARK 500 LEU A 84 58.28 -119.68 REMARK 500 ARG A 96 -32.20 41.46 REMARK 500 SER A 113 107.17 -2.25 REMARK 500 GLN A 135 16.15 -51.51 REMARK 500 PRO A 138 33.31 -12.87 REMARK 500 HIS A 143 59.64 -105.01 REMARK 500 GLU A 157 -150.01 -126.19 REMARK 500 ASP A 158 -173.87 71.12 REMARK 500 TYR A 160 5.28 -69.29 REMARK 500 ASP A 168 14.48 89.10 REMARK 500 LYS A 186 -146.30 -100.83 REMARK 500 LYS A 187 -15.22 58.45 REMARK 500 PHE A 190 76.70 -119.08 REMARK 500 PRO A 191 -9.76 -47.42 REMARK 500 GLU A 203 -70.05 -70.59 REMARK 500 GLU A 215 -17.90 -39.56 REMARK 500 LYS A 230 59.47 -97.23 REMARK 500 ASN A 232 -16.66 -152.30 REMARK 500 MET A 234 79.39 -112.10 REMARK 500 PHE A 236 -169.11 -100.78 REMARK 500 THR A 237 -83.75 44.78 REMARK 500 GLU A 251 -75.21 -82.28 REMARK 500 ILE A 258 63.79 -69.08 REMARK 500 ASP A 259 -63.73 64.67 REMARK 500 PRO A 262 -61.63 -12.01 REMARK 500 PRO A 269 -79.79 -68.56 REMARK 500 ASN A 270 9.84 -60.71 REMARK 500 THR A 271 -30.24 -153.79 REMARK 500 ALA A 282 -42.46 -23.45 REMARK 500 ILE A 289 1.68 -61.95 REMARK 500 ALA A 294 -5.58 65.40 REMARK 500 ASP A 297 -78.35 -143.40 REMARK 500 ILE A 320 -58.67 -15.89 REMARK 500 GLU A 331 95.35 -68.26 REMARK 500 CYS A 332 -166.67 54.01 REMARK 500 ALA A 342 78.02 12.67 REMARK 500 ALA A 346 -115.60 -69.45 REMARK 500 REMARK 500 THIS ENTRY HAS 59 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 112 SER A 113 -149.08 REMARK 500 GLY A 261 PRO A 262 -122.85 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 31 0.10 SIDE CHAIN REMARK 500 TYR A 69 0.10 SIDE CHAIN REMARK 500 TYR A 125 0.08 SIDE CHAIN REMARK 500 TYR A 134 0.10 SIDE CHAIN REMARK 500 TYR A 296 0.10 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 CA A 417 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 307 OD1 REMARK 620 2 ASP A 311 OD1 93.9 REMARK 620 3 ASP A 311 OD2 99.7 71.1 REMARK 620 4 AKG A 418 O2 51.8 112.2 150.9 REMARK 620 5 AKG A 418 O5 92.6 158.2 87.3 88.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 418 DBREF 1IKA 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 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 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 CA A 417 1 HET AKG A 418 10 HETNAM CA CALCIUM ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 CA CA 2+ FORMUL 3 AKG C5 H6 O5 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 OD1 ASP A 307 CA CA A 417 1555 1555 2.65 LINK OD1 ASP A 311 CA CA A 417 1555 1555 1.98 LINK OD2 ASP A 311 CA CA A 417 1555 1555 1.53 LINK CA CA A 417 O2 AKG A 418 1555 1555 1.71 LINK CA CA A 417 O5 AKG A 418 1555 1555 1.88 SITE 1 AC1 3 ASP A 307 ASP A 311 AKG A 418 SITE 1 AC2 9 SER A 113 ASN A 115 ARG A 119 ARG A 129 SITE 2 AC2 9 LYS A 230 ASP A 283 ASP A 307 ASP A 311 SITE 3 AC2 9 CA 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