HEADER OXIDOREDUCTASE 30-APR-97 1AI2 TITLE ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM TITLE 2 (FLASH-COOLED) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OXALOSUCCINATE DECARBOXYLASE, IDH; COMPND 5 EC: 1.1.1.42; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 CELL_LINE: DEK2004; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PICD KEYWDS OXIDOREDUCTASE (NAD(A)-CHOH(D)), NADP, PHOSPHORYLATION, GLYOXYLATE KEYWDS 2 BYPASS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.L.STODDARD,A.MESECAR,D.E.KOSHLAND JUNIOR REVDAT 6 25-DEC-24 1AI2 1 REMARK LINK REVDAT 5 02-AUG-23 1AI2 1 REMARK LINK REVDAT 4 13-JUL-11 1AI2 1 VERSN REVDAT 3 24-FEB-09 1AI2 1 VERSN REVDAT 2 01-APR-03 1AI2 1 JRNL REVDAT 1 15-OCT-97 1AI2 0 SPRSDE 15-OCT-97 1AI2 1IKB JRNL AUTH A.D.MESECAR,B.L.STODDARD,D.E.KOSHLAND JR. JRNL TITL ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL JRNL TITL 2 STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES. JRNL REF SCIENCE V. 277 202 1997 JRNL REFN ISSN 0036-8075 JRNL PMID 9211842 JRNL DOI 10.1126/SCIENCE.277.5323.202 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.H.HURLEY,R.CHEN,A.M.DEAN REMARK 1 TITL DETERMINANTS OF COFACTOR SPECIFICITY IN ISOCITRATE REMARK 1 TITL 2 DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP+--> NAD+ REMARK 1 TITL 3 SPECIFICITY-REVERSAL MUTANT REMARK 1 REF BIOCHEMISTRY V. 35 5670 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.L.STODDARD,A.DEAN,D.E.KOSHLAND JUNIOR REMARK 1 TITL STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ISOCITRATE, REMARK 1 TITL 2 NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE, AND CALCIUM AT REMARK 1 TITL 3 2.5-A RESOLUTION: A PSEUDO-MICHAELIS TERNARY COMPLEX REMARK 1 REF BIOCHEMISTRY V. 32 9310 1993 REMARK 1 REFN ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 63007 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) : 0.191 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3150 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 : 62 REMARK 3 SOLVENT ATOMS : 304 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.40 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.550 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1AI2 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_1000170842. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TORROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.14000 REMARK 200 R SYM FOR SHELL (I) : 0.14000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1ISO REMARK 200 REMARK 200 REMARK: RESIDUES MUTATED IN 1ISO CHANGED BACK TO WILD TYPE REMARK 200 SEQUENCE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.30 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 75.25000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.15000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.87500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.15000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.62500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.15000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.87500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.15000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.15000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.62500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 75.25000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 9890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 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 CZ TYR A 391 O HOH A 481 0.81 REMARK 500 CE1 TYR A 391 O HOH A 481 0.96 REMARK 500 NH1 ARG A 132 O HOH A 558 1.24 REMARK 500 CE2 TYR A 391 O HOH A 490 1.52 REMARK 500 CE2 TYR A 391 O HOH A 481 1.65 REMARK 500 CD2 TYR A 391 O HOH A 490 1.67 REMARK 500 ND2 ASN A 220 O HOH A 711 1.71 REMARK 500 OE1 GLU A 203 O HOH A 599 1.73 REMARK 500 OD1 ASN A 220 O HOH A 610 1.73 REMARK 500 OG SER A 156 O HOH A 686 1.76 REMARK 500 CE LYS A 344 O HOH A 470 1.77 REMARK 500 O GLU A 157 N ASP A 158 1.79 REMARK 500 CD1 TYR A 391 O HOH A 481 1.81 REMARK 500 NE ARG A 395 O HOH A 483 1.99 REMARK 500 OH TYR A 391 O HOH A 481 2.01 REMARK 500 NH2 ARG A 395 O HOH A 483 2.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CE1 PHE A 190 OE1 GLU A 204 7555 1.96 REMARK 500 O PRO A 140 NZ LYS A 142 7555 2.08 REMARK 500 OE2 GLU A 157 CB ARG A 189 7555 2.11 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 TRP A 65 NE1 TRP A 65 CE2 0.114 REMARK 500 TRP A 83 NE1 TRP A 83 CE2 0.115 REMARK 500 TRP A 165 NE1 TRP A 165 CE2 0.114 REMARK 500 TRP A 165 C LYS A 166 N -0.172 REMARK 500 TRP A 244 NE1 TRP A 244 CE2 0.113 REMARK 500 TRP A 263 NE1 TRP A 263 CE2 0.113 REMARK 500 TRP A 369 NE1 TRP A 369 CE2 0.114 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 SER A 3 O - C - N ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG A 132 O - C - N ANGL. DEV. = -10.3 DEGREES REMARK 500 GLU A 157 O - C - N ANGL. DEV. = -37.1 DEGREES REMARK 500 GLU A 164 O - C - N ANGL. DEV. = -9.8 DEGREES REMARK 500 TRP A 165 C - N - CA ANGL. DEV. = 15.8 DEGREES REMARK 500 PRO A 191 C - N - CA ANGL. DEV. = 10.6 DEGREES REMARK 500 PRO A 293 C - N - CA ANGL. DEV. = 9.0 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 ILE A 37 1.32 -67.91 REMARK 500 GLN A 80 -81.19 -17.92 REMARK 500 ARG A 96 -47.99 69.71 REMARK 500 SER A 113 123.42 -33.03 REMARK 500 ASP A 158 170.88 116.13 REMARK 500 ASP A 168 -5.24 67.26 REMARK 500 ASP A 259 -134.97 57.71 REMARK 500 ASP A 297 -95.87 -138.30 REMARK 500 ALA A 342 60.51 38.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ARG A 132 15.02 REMARK 500 GLU A 157 41.04 REMARK 500 ARG A 211 -11.90 REMARK 500 LYS A 230 12.85 REMARK 500 ASP A 297 -10.09 REMARK 500 ASP A 311 -10.46 REMARK 500 GLN A 316 -13.46 REMARK 500 GLU A 331 -10.11 REMARK 500 LYS A 350 -13.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 736 DISTANCE = 6.18 ANGSTROMS REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 ICA A 418 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 ICA A 418 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD2 REMARK 620 2 ICA A 418 O7 81.0 REMARK 620 3 ASP A 307 OD1 71.1 80.0 REMARK 620 4 ASP A 311 OD2 62.3 143.1 84.4 REMARK 620 5 ASP A 311 OD1 106.9 160.3 85.5 46.8 REMARK 620 6 HOH A 458 O 148.3 111.5 138.2 102.4 71.4 REMARK 620 7 HOH A 459 O 82.0 108.1 150.4 72.2 91.1 66.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICA A 418 DBREF 1AI2 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 NAP A 417 48 HET ICA A 418 14 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM ICA ISOCITRATE CALCIUM COMPLEX HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 ICA C6 H7 CA O7 FORMUL 4 HOH *304(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 ILE A 159 ALA A 161 5 3 HELIX 7 7 ALA A 170 GLU A 181 1 12 HELIX 8 8 GLU A 203 ALA A 219 1 17 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 GLY A 354 HIS A 366 1 13 HELIX 14 14 THR A 370 ASN A 385 1 16 HELIX 15 15 TYR A 391 LEU A 396 1 6 HELIX 16 16 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 GLU A 67 0 SHEET 2 B11 ILE A 28 ILE A 32 1 N ILE A 29 O SER A 64 SHEET 3 B11 VAL A 97 LYS A 100 1 N ILE A 99 O PRO A 30 SHEET 4 B11 ALA A 333 GLU A 336 1 N ALA A 333 O ALA A 98 SHEET 5 B11 ALA A 326 ILE A 328 -1 N ASN A 327 O LEU A 334 SHEET 6 B11 ILE A 126 ARG A 132 -1 N LEU A 128 O ALA A 326 SHEET 7 B11 ASP A 148 GLU A 154 -1 N ARG A 153 O CYS A 127 SHEET 8 B11 VAL A 298 CYS A 301 1 N ILE A 299 O VAL A 150 SHEET 9 B11 SER A 224 HIS A 229 1 N THR A 226 O VAL A 298 SHEET 10 B11 GLU A 274 ILE A 281 1 N VAL A 276 O VAL A 225 SHEET 11 B11 LEU A 264 LYS A 267 -1 N VAL A 266 O ILE A 275 LINK OD2 ASP A 283 CA ICA A 418 7555 1555 2.44 LINK OD1 ASP A 307 CA ICA A 418 1555 1555 2.66 LINK OD2 ASP A 311 CA ICA A 418 1555 1555 2.34 LINK OD1 ASP A 311 CA ICA A 418 1555 1555 2.93 LINK CA ICA A 418 O HOH A 458 1555 1555 2.47 LINK CA ICA A 418 O HOH A 459 1555 1555 2.56 CISPEP 1 GLY A 261 PRO A 262 0 10.38 SITE 1 AC1 21 ILE A 37 LYS A 58 LYS A 100 LEU A 103 SITE 2 AC1 21 THR A 104 ALA A 337 THR A 338 HIS A 339 SITE 3 AC1 21 GLY A 340 THR A 341 ALA A 342 PRO A 343 SITE 4 AC1 21 TYR A 345 VAL A 351 ASN A 352 TYR A 391 SITE 5 AC1 21 ASP A 392 ARG A 395 ICA A 418 HOH A 470 SITE 6 AC1 21 HOH A 491 SITE 1 AC2 14 SER A 113 ASN A 115 ARG A 119 ARG A 129 SITE 2 AC2 14 ARG A 153 TYR A 160 LYS A 230 ILE A 233 SITE 3 AC2 14 ASP A 283 ASP A 307 ASP A 311 NAP A 417 SITE 4 AC2 14 HOH A 458 HOH A 459 CRYST1 102.300 102.300 150.500 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009775 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006645 0.00000