HEADER OXIDOREDUCTASE 23-JUL-98 1BL5
TITLE ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE
TITLE 2 OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION
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 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: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTK513;
SOURCE 10 EXPRESSION_SYSTEM_GENE: ICD
KEYWDS OXIDOREDUCTASE, NAD(A)-CHOH(D), PHOSPHORYLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR B.L.STODDARD,B.COHEN,M.BRUBAKER,A.MESECAR,D.E.KOSHLAND JUNIOR
REVDAT 5 07-FEB-24 1BL5 1 REMARK LINK
REVDAT 4 13-JUL-11 1BL5 1 VERSN
REVDAT 3 24-FEB-09 1BL5 1 VERSN
REVDAT 2 01-APR-03 1BL5 1 JRNL
REVDAT 1 04-MAY-99 1BL5 0
JRNL AUTH B.L.STODDARD,B.E.COHEN,M.BRUBAKER,A.D.MESECAR,
JRNL AUTH 2 D.E.KOSHLAND JR.
JRNL TITL MILLISECOND LAUE STRUCTURES OF AN ENZYME-PRODUCT COMPLEX
JRNL TITL 2 USING PHOTOCAGED SUBSTRATE ANALOGS.
JRNL REF NAT.STRUCT.BIOL. V. 5 891 1998
JRNL REFN ISSN 1072-8368
JRNL PMID 9783749
JRNL DOI 10.1038/2331
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 3.8
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) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.8
REMARK 3 NUMBER OF REFLECTIONS : 27430
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) : 0.222
REMARK 3 FREE R VALUE : 0.271
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1372
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.020
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 : 3196
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 38
REMARK 3 SOLVENT ATOMS : 83
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) : 0.017
REMARK 3 BOND ANGLES (DEGREES) : 2.800
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
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 1BL5 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_1000171880.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JAN-95
REMARK 200 TEMPERATURE (KELVIN) : 274
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 6
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
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 : LAUEVIEW, LAUEGEN
REMARK 200 DATA SCALING SOFTWARE : LAUEVIEW, LAUEGEN
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21751
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.8
REMARK 200 DATA REDUNDANCY : 12.90
REMARK 200 R MERGE (I) : 0.10200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50
REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8
REMARK 200 DATA REDUNDANCY IN SHELL : 16.40
REMARK 200 R MERGE FOR SHELL (I) : 0.23700
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.500
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: LAUE
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER
REMARK 200 SOFTWARE USED: X-PLOR 3.8
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 74.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.70
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5
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 75.90000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 53.05000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 53.05000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 113.85000
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 53.05000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 53.05000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.95000
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 53.05000
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.05000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.85000
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 53.05000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.05000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.95000
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 75.90000
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: 9190 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 32220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 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 SER A 74 CA SER A 74 CB -0.095
REMARK 500 HIS A 143 NE2 HIS A 143 CD2 -0.069
REMARK 500 HIS A 193 NE2 HIS A 193 CD2 -0.079
REMARK 500 CYS A 201 CA CYS A 201 CB -0.079
REMARK 500 HIS A 229 NE2 HIS A 229 CD2 -0.075
REMARK 500 HIS A 339 NE2 HIS A 339 CD2 -0.067
REMARK 500 HIS A 366 NE2 HIS A 366 CD2 -0.074
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 LYS A 13 CA - CB - CG ANGL. DEV. = 14.4 DEGREES
REMARK 500 GLU A 25 CA - CB - CG ANGL. DEV. = 13.5 DEGREES
REMARK 500 VAL A 48 CG1 - CB - CG2 ANGL. DEV. = -10.3 DEGREES
REMARK 500 LYS A 55 CB - CG - CD ANGL. DEV. = 17.9 DEGREES
REMARK 500 ARG A 61 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 TRP A 65 CD1 - CG - CD2 ANGL. DEV. = 7.0 DEGREES
REMARK 500 TRP A 65 CB - CG - CD1 ANGL. DEV. = -8.6 DEGREES
REMARK 500 TRP A 65 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES
REMARK 500 TRP A 83 CD1 - CG - CD2 ANGL. DEV. = 5.7 DEGREES
REMARK 500 TRP A 83 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES
REMARK 500 LEU A 103 CA - CB - CG ANGL. DEV. = 15.9 DEGREES
REMARK 500 ARG A 112 CG - CD - NE ANGL. DEV. = 13.4 DEGREES
REMARK 500 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 ARG A 112 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES
REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES
REMARK 500 VAL A 150 CG1 - CB - CG2 ANGL. DEV. = -12.6 DEGREES
REMARK 500 ILE A 151 CG1 - CB - CG2 ANGL. DEV. = -13.8 DEGREES
REMARK 500 ARG A 153 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 TYR A 160 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES
REMARK 500 TRP A 165 CD1 - CG - CD2 ANGL. DEV. = 7.7 DEGREES
REMARK 500 TRP A 165 CE2 - CD2 - CG ANGL. DEV. = -6.2 DEGREES
REMARK 500 ARG A 180 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES
REMARK 500 ARG A 222 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ARG A 222 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES
REMARK 500 ASP A 223 CA - C - N ANGL. DEV. = 14.1 DEGREES
REMARK 500 ASP A 223 O - C - N ANGL. DEV. = -10.2 DEGREES
REMARK 500 TRP A 244 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES
REMARK 500 TRP A 244 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES
REMARK 500 TRP A 244 CG - CD2 - CE3 ANGL. DEV. = 5.4 DEGREES
REMARK 500 TRP A 263 CD1 - CG - CD2 ANGL. DEV. = 4.9 DEGREES
REMARK 500 TRP A 263 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500 VAL A 280 CG1 - CB - CG2 ANGL. DEV. = -10.5 DEGREES
REMARK 500 LEU A 290 CB - CG - CD2 ANGL. DEV. = -10.9 DEGREES
REMARK 500 PRO A 324 C - N - CA ANGL. DEV. = 9.8 DEGREES
REMARK 500 MET A 363 CG - SD - CE ANGL. DEV. = 10.8 DEGREES
REMARK 500 TRP A 369 CD1 - CG - CD2 ANGL. DEV. = 4.8 DEGREES
REMARK 500 TRP A 369 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES
REMARK 500 THR A 388 CA - CB - OG1 ANGL. DEV. = -13.1 DEGREES
REMARK 500 THR A 388 CA - CB - CG2 ANGL. DEV. = 8.5 DEGREES
REMARK 500 VAL A 389 N - CA - CB ANGL. DEV. = -15.3 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 26 71.25 -112.87
REMARK 500 LYS A 58 27.37 39.61
REMARK 500 ARG A 96 -23.60 59.80
REMARK 500 ARG A 112 -98.07 -72.52
REMARK 500 GLU A 157 -146.94 -135.24
REMARK 500 ASP A 158 178.06 73.29
REMARK 500 ILE A 159 -13.77 -39.06
REMARK 500 HIS A 193 41.79 36.14
REMARK 500 LYS A 230 58.11 -101.26
REMARK 500 MET A 234 79.81 -113.52
REMARK 500 ASP A 259 -106.28 38.69
REMARK 500 THR A 271 -22.93 -143.48
REMARK 500 ASP A 297 -89.64 -149.96
REMARK 500 TRP A 369 57.45 -91.89
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 0.08 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 610
REMARK 610 MISSING HETEROATOM
REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 610 I=INSERTION CODE):
REMARK 610 M RES C SSEQI
REMARK 610 NAP A 2
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 418 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 AKG A 1 O2
REMARK 620 2 AKG A 1 O5 71.2
REMARK 620 3 ASP A 283 OD2 147.7 77.7
REMARK 620 4 ASP A 307 OD1 109.1 103.5 69.9
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: SUB
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: SUBSTRATE/PRODUCT BINDING SITE
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 418
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 1
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 2
DBREF 1BL5 A 3 416 UNP P08200 IDH_ECOLI 3 416
SEQRES 1 A 414 SER LYS VAL VAL VAL PRO ALA GLN GLY LYS LYS ILE THR
SEQRES 2 A 414 LEU GLN ASN GLY LYS LEU ASN VAL PRO GLU ASN PRO ILE
SEQRES 3 A 414 ILE PRO TYR ILE GLU GLY ASP GLY ILE GLY VAL ASP VAL
SEQRES 4 A 414 THR PRO ALA MET LEU LYS VAL VAL ASP ALA ALA VAL GLU
SEQRES 5 A 414 LYS ALA TYR LYS GLY GLU ARG LYS ILE SER TRP MET GLU
SEQRES 6 A 414 ILE TYR THR GLY GLU LYS SER THR GLN VAL TYR GLY GLN
SEQRES 7 A 414 ASP VAL TRP LEU PRO ALA GLU THR LEU ASP LEU ILE ARG
SEQRES 8 A 414 GLU TYR ARG VAL ALA ILE LYS GLY PRO LEU THR THR PRO
SEQRES 9 A 414 VAL GLY GLY GLY ILE ARG SER LEU ASN VAL ALA LEU ARG
SEQRES 10 A 414 GLN GLU LEU ASP LEU TYR ILE CYS LEU ARG PRO VAL ARG
SEQRES 11 A 414 TYR TYR GLN GLY THR PRO SER PRO VAL LYS HIS PRO GLU
SEQRES 12 A 414 LEU THR ASP MET VAL ILE PHE ARG GLU ASN SER GLU ASP
SEQRES 13 A 414 ILE TYR ALA GLY ILE GLU TRP LYS ALA ASP SER ALA ASP
SEQRES 14 A 414 ALA GLU LYS VAL ILE LYS PHE LEU ARG GLU GLU MET GLY
SEQRES 15 A 414 VAL LYS LYS ILE ARG PHE PRO GLU HIS CYS GLY ILE GLY
SEQRES 16 A 414 ILE LYS PRO CYS SER GLU GLU GLY THR LYS ARG LEU VAL
SEQRES 17 A 414 ARG ALA ALA ILE GLU TYR ALA ILE ALA ASN ASP ARG ASP
SEQRES 18 A 414 SER VAL THR LEU VAL HIS LYS GLY ASN ILE MET LYS PHE
SEQRES 19 A 414 THR GLU GLY ALA PHE LYS ASP TRP GLY TYR GLN LEU ALA
SEQRES 20 A 414 ARG GLU GLU PHE GLY GLY GLU LEU ILE ASP GLY GLY PRO
SEQRES 21 A 414 TRP LEU LYS VAL LYS ASN PRO ASN THR GLY LYS GLU ILE
SEQRES 22 A 414 VAL ILE LYS ASP VAL ILE ALA ASP ALA PHE LEU GLN GLN
SEQRES 23 A 414 ILE LEU LEU ARG PRO ALA GLU TYR ASP VAL ILE ALA CYS
SEQRES 24 A 414 MET ASN LEU ASN GLY ASP TYR ILE SER ASP ALA LEU ALA
SEQRES 25 A 414 ALA GLN VAL GLY GLY ILE GLY ILE ALA PRO GLY ALA ASN
SEQRES 26 A 414 ILE GLY ASP GLU CYS ALA LEU PHE GLU ALA THR HIS GLY
SEQRES 27 A 414 THR ALA PRO LYS TYR ALA GLY GLN ASP LYS VAL ASN PRO
SEQRES 28 A 414 GLY SER ILE ILE LEU SER ALA GLU MET MET LEU ARG HIS
SEQRES 29 A 414 MET GLY TRP THR GLU ALA ALA ASP LEU ILE VAL LYS GLY
SEQRES 30 A 414 MET GLU GLY ALA ILE ASN ALA LYS THR VAL THR TYR ASP
SEQRES 31 A 414 PHE GLU ARG LEU MET ASP GLY ALA LYS LEU LEU LYS CYS
SEQRES 32 A 414 SER GLU PHE GLY ASP ALA ILE ILE GLU ASN MET
HET MG A 418 1
HET AKG A 1 10
HET NAP A 2 27
HETNAM MG MAGNESIUM ION
HETNAM AKG 2-OXOGLUTARIC ACID
HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
FORMUL 2 MG MG 2+
FORMUL 3 AKG C5 H6 O5
FORMUL 4 NAP C21 H28 N7 O17 P3
FORMUL 5 HOH *83(H2 O)
HELIX 1 1 GLY A 36 TYR A 57 5 22
HELIX 2 2 GLU A 72 TYR A 78 1 7
HELIX 3 3 ALA A 86 TYR A 95 1 10
HELIX 4 4 LEU A 114 GLU A 121 1 8
HELIX 5 5 PRO A 144 LEU A 146 5 3
HELIX 6 6 ASP A 158 ALA A 161 5 4
HELIX 7 7 ALA A 170 GLU A 181 1 12
HELIX 8 8 GLU A 203 ASN A 220 1 18
HELIX 9 9 GLU A 238 PHE A 253 1 16
HELIX 10 10 ALA A 282 LEU A 291 1 10
HELIX 11 11 PRO A 293 GLU A 295 5 3
HELIX 12 12 ASN A 303 GLN A 316 1 14
HELIX 13 13 PRO A 343 TYR A 345 5 3
HELIX 14 14 GLY A 354 MET A 367 1 14
HELIX 15 15 THR A 370 ASN A 385 1 16
HELIX 16 16 TYR A 391 LEU A 396 1 6
HELIX 17 17 CYS A 405 GLU A 414 1 10
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 ILE A 68 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 ALA A 337 1 N ALA A 333 O ALA A 98
SHEET 5 B11 PRO A 324 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 O2 AKG A 1 MG MG A 418 1555 1555 2.21
LINK O5 AKG A 1 MG MG A 418 1555 1555 2.09
LINK OD2 ASP A 283 MG MG A 418 7555 1555 2.35
LINK OD1 ASP A 307 MG MG A 418 1555 1555 2.40
CISPEP 1 GLY A 261 PRO A 262 0 5.28
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 AKG A 1 ASP A 283 ASP A 307 ASP A 311
SITE 1 AC2 9 SER A 113 ASN A 115 ARG A 119 ARG A 129
SITE 2 AC2 9 ARG A 153 LYS A 230 ASP A 283 ASP A 307
SITE 3 AC2 9 MG A 418
SITE 1 AC3 7 HIS A 339 GLY A 340 THR A 341 ALA A 342
SITE 2 AC3 7 TYR A 345 ASN A 352 TYR A 391
CRYST1 106.100 106.100 151.800 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 0.009425 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009425 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006588 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
