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 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 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