HEADER OXIDOREDUCTASE 24-MAR-10 3MAR TITLE CRYSTAL STRUCTURE OF HOMODIMERIC R132H MUTANT OF HUMAN CYTOSOLIC TITLE 2 NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH NADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP] CYTOPLASMIC; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: IDH, CYTOSOLIC NADP-ISOCITRATE DEHYDROGENASE, OXALOSUCCINATE COMPND 5 DECARBOXYLASE, NADP(+)-SPECIFIC ICDH, IDP; COMPND 6 EC: 1.1.1.42; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IDH1, PICD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET KEYWDS ISOCITRATE DEHYDROGENASE, NICOTINAMIDE ADENINE DINUCLEOTIDE KEYWDS 2 PHOSPHATE, ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR B.YANG,Y.PENG,J.DING REVDAT 2 21-MAY-14 3MAR 1 JRNL VERSN REVDAT 1 10-NOV-10 3MAR 0 JRNL AUTH B.YANG,C.ZHONG,Y.PENG,Z.LAI,J.DING JRNL TITL MOLECULAR MECHANISMS OF "OFF-ON SWITCH" OF ACTIVITIES OF JRNL TITL 2 HUMAN IDH1 BY TUMOR-ASSOCIATED MUTATION R132H. JRNL REF CELL RES. V. 20 1188 2010 JRNL REFN ISSN 1001-0602 JRNL PMID 20975740 JRNL DOI 10.1038/CR.2010.145 REMARK 2 REMARK 2 RESOLUTION. 3.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.41 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) (%) : 91.3 REMARK 3 NUMBER OF REFLECTIONS : 14202 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) : 0.245 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 720 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.52 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1154 REMARK 3 BIN R VALUE (WORKING SET) : 0.3105 REMARK 3 BIN FREE R VALUE : 0.3516 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 57 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 : 6238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 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) : 89.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 9.57500 REMARK 3 B22 (A**2) : 9.57500 REMARK 3 B33 (A**2) : -19.15100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.249 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 5.300 REMARK 3 IMPROPER ANGLES (DEGREES) : 40.270 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) : 0.277 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 0.539 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : MASK REMARK 3 KSOL : NULL REMARK 3 BSOL : 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: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3MAR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-10. REMARK 100 THE RCSB ID CODE IS RCSB058320. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14215 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.400 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 (%) : 91.2 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.18300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.56100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1T09 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M NA2HPO4/KH2PO4, PH 8.2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 153.05800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.54950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.54950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 229.58700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.54950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.54950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.52900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.54950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.54950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 229.58700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.54950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.54950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.52900 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 153.05800 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 REMARK 350 TOTAL BURIED SURFACE AREA: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 TYR A 135 REMARK 465 GLY A 136 REMARK 465 ASP A 137 REMARK 465 GLN A 138 REMARK 465 TYR A 139 REMARK 465 ARG A 140 REMARK 465 MET A 259 REMARK 465 LYS A 260 REMARK 465 TYR A 272 REMARK 465 ASP A 273 REMARK 465 GLY A 274 REMARK 465 ASP A 275 REMARK 465 VAL A 276 REMARK 465 GLN A 277 REMARK 465 SER A 278 REMARK 465 ASP A 279 REMARK 465 SER A 280 REMARK 465 VAL A 281 REMARK 465 ALA A 282 REMARK 465 GLN A 283 REMARK 465 LEU A 415 REMARK 465 GLU A 416 REMARK 465 HIS A 417 REMARK 465 HIS A 418 REMARK 465 HIS A 419 REMARK 465 HIS A 420 REMARK 465 HIS A 421 REMARK 465 HIS A 422 REMARK 465 TYR B 135 REMARK 465 GLY B 136 REMARK 465 ASP B 137 REMARK 465 GLN B 138 REMARK 465 TYR B 139 REMARK 465 TYR B 272 REMARK 465 ASP B 273 REMARK 465 GLY B 274 REMARK 465 ASP B 275 REMARK 465 VAL B 276 REMARK 465 GLN B 277 REMARK 465 SER B 278 REMARK 465 ASP B 279 REMARK 465 SER B 280 REMARK 465 VAL B 281 REMARK 465 ALA B 282 REMARK 465 GLN B 283 REMARK 465 GLY B 284 REMARK 465 TYR B 285 REMARK 465 LEU B 415 REMARK 465 GLU B 416 REMARK 465 HIS B 417 REMARK 465 HIS B 418 REMARK 465 HIS B 419 REMARK 465 HIS B 420 REMARK 465 HIS B 421 REMARK 465 HIS B 422 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 O ALA A 377 O ILE A 380 2.19 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 4 132.29 -25.26 REMARK 500 GLU A 17 -172.02 64.55 REMARK 500 GLU A 24 35.66 -73.97 REMARK 500 LEU A 25 -32.45 -144.73 REMARK 500 ILE A 31 -69.17 -101.38 REMARK 500 ASP A 38 58.77 -90.16 REMARK 500 ILE A 46 -52.27 -29.09 REMARK 500 ASP A 54 -5.20 57.53 REMARK 500 ASN A 68 -12.00 74.14 REMARK 500 ASP A 79 -157.84 -130.00 REMARK 500 LYS A 87 39.89 82.21 REMARK 500 LYS A 93 -163.07 -65.85 REMARK 500 VAL A 121 75.32 60.25 REMARK 500 SER A 122 93.42 -56.84 REMARK 500 VAL A 125 -61.23 -90.65 REMARK 500 VAL A 146 71.98 45.87 REMARK 500 LEU A 168 105.92 72.47 REMARK 500 VAL A 169 69.04 -104.68 REMARK 500 HIS A 170 124.97 51.62 REMARK 500 VAL A 178 145.31 -171.91 REMARK 500 TYR A 183 -179.18 -171.57 REMARK 500 THR A 211 -154.25 -123.71 REMARK 500 LYS A 212 45.02 -152.27 REMARK 500 TYR A 219 -69.89 -94.41 REMARK 500 PHE A 227 -72.72 -69.76 REMARK 500 TYR A 235 -6.56 74.63 REMARK 500 ARG A 249 -111.51 -92.29 REMARK 500 LEU A 250 130.67 164.45 REMARK 500 ALA A 256 -69.77 -92.70 REMARK 500 SER A 287 -173.34 49.02 REMARK 500 ASP A 299 -29.03 -24.88 REMARK 500 HIS A 309 -49.43 -133.29 REMARK 500 ASN A 349 79.16 -100.54 REMARK 500 LYS A 381 23.95 86.21 REMARK 500 SER A 389 5.51 -64.92 REMARK 500 SER B 2 -75.26 169.72 REMARK 500 GLU B 17 -138.43 45.26 REMARK 500 HIS B 40 72.99 -104.23 REMARK 500 ASN B 68 -25.45 77.02 REMARK 500 ALA B 74 -153.20 -69.48 REMARK 500 THR B 75 138.86 166.07 REMARK 500 MET B 91 79.80 -100.64 REMARK 500 TRP B 124 108.19 -54.14 REMARK 500 ASP B 160 42.49 -166.01 REMARK 500 GLN B 163 145.57 168.87 REMARK 500 HIS B 170 147.08 165.48 REMARK 500 HIS B 194 -73.17 -42.78 REMARK 500 SER B 196 42.73 -90.32 REMARK 500 PHE B 197 -38.12 -146.28 REMARK 500 LEU B 216 59.95 -108.37 REMARK 500 REMARK 500 THIS ENTRY HAS 56 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL A 145 24.3 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL 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 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MAP RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HOMODIMERIC R132H MUTANT OF HUMAN REMARK 900 CYTOSOLIC NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN REMARK 900 COMPLEX WITH NADP AND ISOCITRATE REMARK 900 RELATED ID: 3MAS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HETERODIMERIC R132H MUTANT OF HUMAN REMARK 900 CYTOSOLIC NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN REMARK 900 COMPLEX WITH NADP AND ISOCITRATE DBREF 3MAR A 1 414 UNP O75874 IDHC_HUMAN 1 414 DBREF 3MAR B 1 414 UNP O75874 IDHC_HUMAN 1 414 SEQADV 3MAR HIS A 132 UNP O75874 ARG 132 ENGINEERED SEQADV 3MAR LEU A 415 UNP O75874 EXPRESSION TAG SEQADV 3MAR GLU A 416 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS A 417 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS A 418 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS A 419 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS A 420 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS A 421 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS A 422 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 132 UNP O75874 ARG 132 ENGINEERED SEQADV 3MAR LEU B 415 UNP O75874 EXPRESSION TAG SEQADV 3MAR GLU B 416 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 417 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 418 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 419 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 420 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 421 UNP O75874 EXPRESSION TAG SEQADV 3MAR HIS B 422 UNP O75874 EXPRESSION TAG SEQRES 1 A 422 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 A 422 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 A 422 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 A 422 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 A 422 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 A 422 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 A 422 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 A 422 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 A 422 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 A 422 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 A 422 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 A 422 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 A 422 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 A 422 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 A 422 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 A 422 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 A 422 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 A 422 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 A 422 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 A 422 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 A 422 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 A 422 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 A 422 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 A 422 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 A 422 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 A 422 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 A 422 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 A 422 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 A 422 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 A 422 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 A 422 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 A 422 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU LEU GLU SEQRES 33 A 422 HIS HIS HIS HIS HIS HIS SEQRES 1 B 422 MET SER LYS LYS ILE SER GLY GLY SER VAL VAL GLU MET SEQRES 2 B 422 GLN GLY ASP GLU MET THR ARG ILE ILE TRP GLU LEU ILE SEQRES 3 B 422 LYS GLU LYS LEU ILE PHE PRO TYR VAL GLU LEU ASP LEU SEQRES 4 B 422 HIS SER TYR ASP LEU GLY ILE GLU ASN ARG ASP ALA THR SEQRES 5 B 422 ASN ASP GLN VAL THR LYS ASP ALA ALA GLU ALA ILE LYS SEQRES 6 B 422 LYS HIS ASN VAL GLY VAL LYS CYS ALA THR ILE THR PRO SEQRES 7 B 422 ASP GLU LYS ARG VAL GLU GLU PHE LYS LEU LYS GLN MET SEQRES 8 B 422 TRP LYS SER PRO ASN GLY THR ILE ARG ASN ILE LEU GLY SEQRES 9 B 422 GLY THR VAL PHE ARG GLU ALA ILE ILE CYS LYS ASN ILE SEQRES 10 B 422 PRO ARG LEU VAL SER GLY TRP VAL LYS PRO ILE ILE ILE SEQRES 11 B 422 GLY HIS HIS ALA TYR GLY ASP GLN TYR ARG ALA THR ASP SEQRES 12 B 422 PHE VAL VAL PRO GLY PRO GLY LYS VAL GLU ILE THR TYR SEQRES 13 B 422 THR PRO SER ASP GLY THR GLN LYS VAL THR TYR LEU VAL SEQRES 14 B 422 HIS ASN PHE GLU GLU GLY GLY GLY VAL ALA MET GLY MET SEQRES 15 B 422 TYR ASN GLN ASP LYS SER ILE GLU ASP PHE ALA HIS SER SEQRES 16 B 422 SER PHE GLN MET ALA LEU SER LYS GLY TRP PRO LEU TYR SEQRES 17 B 422 LEU SER THR LYS ASN THR ILE LEU LYS LYS TYR ASP GLY SEQRES 18 B 422 ARG PHE LYS ASP ILE PHE GLN GLU ILE TYR ASP LYS GLN SEQRES 19 B 422 TYR LYS SER GLN PHE GLU ALA GLN LYS ILE TRP TYR GLU SEQRES 20 B 422 HIS ARG LEU ILE ASP ASP MET VAL ALA GLN ALA MET LYS SEQRES 21 B 422 SER GLU GLY GLY PHE ILE TRP ALA CYS LYS ASN TYR ASP SEQRES 22 B 422 GLY ASP VAL GLN SER ASP SER VAL ALA GLN GLY TYR GLY SEQRES 23 B 422 SER LEU GLY MET MET THR SER VAL LEU VAL CYS PRO ASP SEQRES 24 B 422 GLY LYS THR VAL GLU ALA GLU ALA ALA HIS GLY THR VAL SEQRES 25 B 422 THR ARG HIS TYR ARG MET TYR GLN LYS GLY GLN GLU THR SEQRES 26 B 422 SER THR ASN PRO ILE ALA SER ILE PHE ALA TRP THR ARG SEQRES 27 B 422 GLY LEU ALA HIS ARG ALA LYS LEU ASP ASN ASN LYS GLU SEQRES 28 B 422 LEU ALA PHE PHE ALA ASN ALA LEU GLU GLU VAL SER ILE SEQRES 29 B 422 GLU THR ILE GLU ALA GLY PHE MET THR LYS ASP LEU ALA SEQRES 30 B 422 ALA CYS ILE LYS GLY LEU PRO ASN VAL GLN ARG SER ASP SEQRES 31 B 422 TYR LEU ASN THR PHE GLU PHE MET ASP LYS LEU GLY GLU SEQRES 32 B 422 ASN LEU LYS ILE LYS LEU ALA GLN ALA LYS LEU LEU GLU SEQRES 33 B 422 HIS HIS HIS HIS HIS HIS HET NAP B1003 48 HET NAP A1003 48 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 3 NAP 2(C21 H28 N7 O17 P3) HELIX 1 1 GLU A 17 ILE A 31 1 15 HELIX 2 2 GLY A 45 THR A 52 1 8 HELIX 3 3 ASP A 54 ASN A 68 1 15 HELIX 4 4 ASP A 79 LYS A 87 1 9 HELIX 5 5 SER A 94 ILE A 99 1 6 HELIX 6 6 ILE A 99 GLY A 104 1 6 HELIX 7 7 GLN A 185 SER A 202 1 18 HELIX 8 8 ASP A 220 LYS A 233 1 14 HELIX 9 9 TYR A 235 ALA A 241 1 7 HELIX 10 10 LEU A 250 ALA A 258 1 9 HELIX 11 11 VAL A 312 GLN A 320 1 9 HELIX 12 12 PRO A 329 ASN A 348 1 20 HELIX 13 13 ASN A 349 ALA A 369 1 21 HELIX 14 14 THR A 373 ALA A 378 1 6 HELIX 15 15 LYS A 381 VAL A 386 1 6 HELIX 16 16 GLN A 387 TYR A 391 5 5 HELIX 17 17 ASN A 393 LEU A 414 1 22 HELIX 18 18 ASP B 16 ILE B 31 1 16 HELIX 19 19 GLY B 45 ASN B 53 1 9 HELIX 20 20 ASP B 54 ASN B 68 1 15 HELIX 21 21 ASP B 79 PHE B 86 1 8 HELIX 22 22 SER B 94 GLY B 104 1 11 HELIX 23 23 GLN B 185 LYS B 203 1 19 HELIX 24 24 TYR B 219 GLN B 234 1 16 HELIX 25 25 TYR B 235 GLN B 242 1 8 HELIX 26 26 ILE B 251 LYS B 260 1 10 HELIX 27 27 SER B 287 GLY B 289 5 3 HELIX 28 28 VAL B 312 LYS B 321 1 10 HELIX 29 29 PRO B 329 ASN B 348 1 20 HELIX 30 30 ASN B 349 GLU B 368 1 20 HELIX 31 31 THR B 373 LYS B 381 1 9 HELIX 32 32 GLY B 382 VAL B 386 5 5 HELIX 33 33 GLN B 387 TYR B 391 5 5 HELIX 34 34 ASN B 393 LYS B 413 1 21 SHEET 1 A 2 ILE A 5 GLY A 8 0 SHEET 2 A 2 VAL A 35 LEU A 37 1 O GLU A 36 N ILE A 5 SHEET 1 B 2 VAL A 11 GLN A 14 0 SHEET 2 B 2 HIS A 40 ASP A 43 1 O TYR A 42 N GLN A 14 SHEET 1 C 4 VAL A 69 LYS A 72 0 SHEET 2 C 4 VAL A 303 ALA A 307 1 O ALA A 305 N GLY A 70 SHEET 3 C 4 MET A 291 VAL A 296 -1 N LEU A 295 O GLU A 304 SHEET 4 C 4 THR A 106 VAL A 107 -1 N THR A 106 O VAL A 296 SHEET 1 D 8 VAL A 69 LYS A 72 0 SHEET 2 D 8 VAL A 303 ALA A 307 1 O ALA A 305 N GLY A 70 SHEET 3 D 8 MET A 291 VAL A 296 -1 N LEU A 295 O GLU A 304 SHEET 4 D 8 ARG A 109 ALA A 111 -1 N GLU A 110 O THR A 292 SHEET 5 D 8 ILE A 128 ILE A 130 -1 O ILE A 130 N ARG A 109 SHEET 6 D 8 PHE A 265 CYS A 269 1 O TRP A 267 N ILE A 129 SHEET 7 D 8 LEU A 207 SER A 210 1 N TYR A 208 O ALA A 268 SHEET 8 D 8 TYR A 246 HIS A 248 1 O GLU A 247 N LEU A 207 SHEET 1 E 4 VAL A 165 THR A 166 0 SHEET 2 E 4 GLY A 150 PRO A 158 -1 N TYR A 156 O VAL A 165 SHEET 3 E 4 GLY B 150 PRO B 158 -1 O GLU B 153 N THR A 155 SHEET 4 E 4 VAL B 165 THR B 166 -1 O VAL B 165 N TYR B 156 SHEET 1 F 4 VAL A 165 THR A 166 0 SHEET 2 F 4 GLY A 150 PRO A 158 -1 N TYR A 156 O VAL A 165 SHEET 3 F 4 GLY B 150 PRO B 158 -1 O GLU B 153 N THR A 155 SHEET 4 F 4 HIS B 170 PHE B 172 -1 O HIS B 170 N VAL B 152 SHEET 1 G 3 MET A 182 ASN A 184 0 SHEET 2 G 3 VAL B 178 GLY B 181 -1 O MET B 180 N MET A 182 SHEET 3 G 3 THR B 142 VAL B 145 -1 N PHE B 144 O ALA B 179 SHEET 1 H 3 VAL B 35 LEU B 39 0 SHEET 2 H 3 ILE B 5 GLN B 14 1 N ILE B 5 O GLU B 36 SHEET 3 H 3 TYR B 42 ASP B 43 1 O TYR B 42 N GLU B 12 SHEET 1 I10 VAL B 35 LEU B 39 0 SHEET 2 I10 ILE B 5 GLN B 14 1 N ILE B 5 O GLU B 36 SHEET 3 I10 VAL B 69 LYS B 72 1 O VAL B 71 N VAL B 11 SHEET 4 I10 VAL B 303 ALA B 307 1 O ALA B 305 N LYS B 72 SHEET 5 I10 MET B 291 VAL B 296 -1 N LEU B 295 O GLU B 304 SHEET 6 I10 THR B 106 ALA B 111 -1 N GLU B 110 O THR B 292 SHEET 7 I10 LYS B 126 HIS B 133 -1 O ILE B 130 N ARG B 109 SHEET 8 I10 GLY B 263 LYS B 270 1 O TRP B 267 N ILE B 129 SHEET 9 I10 LEU B 207 THR B 211 1 N TYR B 208 O ALA B 268 SHEET 10 I10 ARG B 249 LEU B 250 1 O ARG B 249 N LEU B 209 SITE 1 AC1 16 LYS A 72 THR A 75 ILE A 76 THR A 77 SITE 2 AC1 16 ARG A 82 GLU A 306 HIS A 309 GLY A 310 SITE 3 AC1 16 THR A 311 VAL A 312 THR A 313 ARG A 314 SITE 4 AC1 16 HIS A 315 THR A 327 ASN A 328 ASP A 375 SITE 1 AC2 17 LYS B 72 THR B 75 ILE B 76 THR B 77 SITE 2 AC2 17 ARG B 82 ASN B 96 LEU B 288 GLY B 289 SITE 3 AC2 17 HIS B 309 GLY B 310 THR B 311 VAL B 312 SITE 4 AC2 17 THR B 313 ARG B 314 HIS B 315 ASN B 328 SITE 5 AC2 17 ASP B 375 CRYST1 83.099 83.099 306.116 90.00 90.00 90.00 P 43 21 2 16 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 0.012034 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012034 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003267 0.00000 MASTER 408 0 2 34 40 0 9 6 0 0 0 66 END