HEADER OXIDOREDUCTASE 01-SEP-22 8GRD TITLE CRYSTAL STRUCTURE OF A CONSTITUTIVELY ACTIVE MUTANT OF THE ALPHA BETA TITLE 2 HETERODIMER OF HUMAN IDH3 IN COMPLEX WITH ADP AND MG COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT ALPHA, COMPND 3 MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: ISOCITRIC DEHYDROGENASE SUBUNIT ALPHA,NAD(+)-SPECIFIC ICDH COMPND 6 SUBUNIT ALPHA; COMPND 7 EC: 1.1.1.41; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ISOFORM A OF ISOCITRATE DEHYDROGENASE [NAD] SUBUNIT BETA, COMPND 11 MITOCHONDRIAL; COMPND 12 CHAIN: B; COMPND 13 SYNONYM: ISOCITRIC DEHYDROGENASE SUBUNIT BETA,NAD(+)-SPECIFIC ICDH COMPND 14 SUBUNIT BETA; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: IDH3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: IDH3B; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ISOCITRATE DEHYDROGENASE, NAD-DEPENDENT IDH, ASSEMBLY, ALLOSTERIC KEYWDS 2 REGULATION, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR X.CHEN,P.SUN,J.DING REVDAT 3 29-NOV-23 8GRD 1 REMARK REVDAT 2 21-DEC-22 8GRD 1 JRNL REVDAT 1 30-NOV-22 8GRD 0 JRNL AUTH X.CHEN,P.SUN,Y.LIU,S.SHEN,T.MA,J.DING JRNL TITL STRUCTURES OF A CONSTITUTIVELY ACTIVE MUTANT OF HUMAN IDH3 JRNL TITL 2 REVEAL NEW INSIGHTS INTO THE MECHANISMS OF ALLOSTERIC JRNL TITL 3 ACTIVATION AND THE CATALYTIC REACTION. JRNL REF J.BIOL.CHEM. V. 298 02695 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36375638 JRNL DOI 10.1016/J.JBC.2022.102695 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 24915 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.3130 - 5.5910 0.97 2718 145 0.1807 0.2050 REMARK 3 2 5.5910 - 4.4478 1.00 2678 142 0.1592 0.1892 REMARK 3 3 4.4478 - 3.8885 1.00 2651 138 0.1682 0.1965 REMARK 3 4 3.8885 - 3.5343 1.00 2612 138 0.1957 0.2710 REMARK 3 5 3.5343 - 3.2817 1.00 2624 138 0.2232 0.3148 REMARK 3 6 3.2817 - 3.0887 1.00 2608 137 0.2304 0.2546 REMARK 3 7 3.0887 - 2.9343 1.00 2606 138 0.2322 0.3190 REMARK 3 8 2.9343 - 2.8068 1.00 2595 137 0.2442 0.3241 REMARK 3 9 2.8068 - 2.6990 0.99 2575 135 0.2474 0.3259 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.15 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 5123 REMARK 3 ANGLE : 1.041 6914 REMARK 3 CHIRALITY : 0.054 790 REMARK 3 PLANARITY : 0.006 886 REMARK 3 DIHEDRAL : 7.834 3122 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8GRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1300031951. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25101 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.699 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 26.30 REMARK 200 R MERGE (I) : 0.14900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 26.00 REMARK 200 R MERGE FOR SHELL (I) : 1.08600 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: PHENIX 1.17.1_3660 REMARK 200 STARTING MODEL: 6KDF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CACODYLATE (PH 5.1), 0.1 REMARK 280 M CALCIUM ACETATE, 10% (W/V) PEG 8000, 4 MM ADP, 4 MM CIT AND REMARK 280 0.4 MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 82.94850 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 64.79150 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 82.94850 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 64.79150 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 82.94850 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 64.79150 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 82.94850 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 64.79150 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 82.94850 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 64.79150 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 82.94850 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 64.79150 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 82.94850 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 64.79150 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 82.94850 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 82.94850 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 64.79150 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: 4740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 THR A 1 REMARK 465 GLY A 2 REMARK 465 GLY A 3 REMARK 465 PRO A 47 REMARK 465 GLY A 48 REMARK 465 GLY A 49 REMARK 465 LYS A 50 REMARK 465 ILE A 76 REMARK 465 ALA A 77 REMARK 465 ALA A 78 REMARK 465 GLY A 79 REMARK 465 HIS A 80 REMARK 465 LEU A 338 REMARK 465 ASP A 339 REMARK 465 ALA B 1 REMARK 465 SER B 2 REMARK 465 ARG B 3 REMARK 465 SER B 4 REMARK 465 GLN B 5 REMARK 465 ALA B 6 REMARK 465 GLU B 7 REMARK 465 ASP B 8 REMARK 465 VAL B 9 REMARK 465 ARG B 10 REMARK 465 VAL B 11 REMARK 465 GLU B 12 REMARK 465 GLY B 13 REMARK 465 SER B 14 REMARK 465 ASN B 56 REMARK 465 THR B 83 REMARK 465 PRO B 84 REMARK 465 MET B 85 REMARK 465 GLU B 86 REMARK 465 TYR B 87 REMARK 465 LYS B 88 REMARK 465 GLY B 89 REMARK 465 GLU B 90 REMARK 465 GLU B 351 REMARK 465 ASN B 352 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 OE2 GLU A 146 O HOH A 501 2.08 REMARK 500 O PHE A 200 O HOH A 502 2.15 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 65 -38.73 69.23 REMARK 500 GLU A 123 -150.62 -134.61 REMARK 500 ASP A 220 -101.08 -116.69 REMARK 500 LYS A 312 3.72 -66.81 REMARK 500 SER A 313 46.90 -156.96 REMARK 500 ASN A 321 28.43 -150.34 REMARK 500 GLU B 53 34.29 70.19 REMARK 500 GLU B 134 -148.30 -141.55 REMARK 500 ARG B 146 109.15 -49.51 REMARK 500 ASN B 226 78.66 -159.53 REMARK 500 ASP B 231 -90.84 -139.98 REMARK 500 SER B 263 -169.58 -116.30 REMARK 500 LEU B 304 59.13 -107.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 230 OD1 REMARK 620 2 ASP A 234 OD1 148.1 REMARK 620 3 ASP B 217 OD2 82.3 85.9 REMARK 620 N 1 2 DBREF 8GRD A 1 339 UNP P50213 IDH3A_HUMAN 28 366 DBREF 8GRD B 1 340 UNP O43837-2 IDH3B_HUMAN 35 374 SEQADV 8GRD ALA A 139 UNP P50213 GLN 166 ENGINEERED MUTATION SEQADV 8GRD GLU B 341 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD ILE B 342 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD CYS B 343 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD ARG B 344 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD ARG B 345 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD VAL B 346 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD LYS B 347 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD ASP B 348 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD LEU B 349 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD ASP B 350 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD GLU B 351 UNP O43837-2 EXPRESSION TAG SEQADV 8GRD ASN B 352 UNP O43837-2 EXPRESSION TAG SEQRES 1 A 339 THR GLY GLY VAL GLN THR VAL THR LEU ILE PRO GLY ASP SEQRES 2 A 339 GLY ILE GLY PRO GLU ILE SER ALA ALA VAL MET LYS ILE SEQRES 3 A 339 PHE ASP ALA ALA LYS ALA PRO ILE GLN TRP GLU GLU ARG SEQRES 4 A 339 ASN VAL THR ALA ILE GLN GLY PRO GLY GLY LYS TRP MET SEQRES 5 A 339 ILE PRO SER GLU ALA LYS GLU SER MET ASP LYS ASN LYS SEQRES 6 A 339 MET GLY LEU LYS GLY PRO LEU LYS THR PRO ILE ALA ALA SEQRES 7 A 339 GLY HIS PRO SER MET ASN LEU LEU LEU ARG LYS THR PHE SEQRES 8 A 339 ASP LEU TYR ALA ASN VAL ARG PRO CYS VAL SER ILE GLU SEQRES 9 A 339 GLY TYR LYS THR PRO TYR THR ASP VAL ASN ILE VAL THR SEQRES 10 A 339 ILE ARG GLU ASN THR GLU GLY GLU TYR SER GLY ILE GLU SEQRES 11 A 339 HIS VAL ILE VAL ASP GLY VAL VAL ALA SER ILE LYS LEU SEQRES 12 A 339 ILE THR GLU GLY ALA SER LYS ARG ILE ALA GLU PHE ALA SEQRES 13 A 339 PHE GLU TYR ALA ARG ASN ASN HIS ARG SER ASN VAL THR SEQRES 14 A 339 ALA VAL HIS LYS ALA ASN ILE MET ARG MET SER ASP GLY SEQRES 15 A 339 LEU PHE LEU GLN LYS CYS ARG GLU VAL ALA GLU SER CYS SEQRES 16 A 339 LYS ASP ILE LYS PHE ASN GLU MET TYR LEU ASP THR VAL SEQRES 17 A 339 CYS LEU ASN MET VAL GLN ASP PRO SER GLN PHE ASP VAL SEQRES 18 A 339 LEU VAL MET PRO ASN LEU TYR GLY ASP ILE LEU SER ASP SEQRES 19 A 339 LEU CYS ALA GLY LEU ILE GLY GLY LEU GLY VAL THR PRO SEQRES 20 A 339 SER GLY ASN ILE GLY ALA ASN GLY VAL ALA ILE PHE GLU SEQRES 21 A 339 SER VAL HIS GLY THR ALA PRO ASP ILE ALA GLY LYS ASP SEQRES 22 A 339 MET ALA ASN PRO THR ALA LEU LEU LEU SER ALA VAL MET SEQRES 23 A 339 MET LEU ARG HIS MET GLY LEU PHE ASP HIS ALA ALA ARG SEQRES 24 A 339 ILE GLU ALA ALA CYS PHE ALA THR ILE LYS ASP GLY LYS SEQRES 25 A 339 SER LEU THR LYS ASP LEU GLY GLY ASN ALA LYS CYS SER SEQRES 26 A 339 ASP PHE THR GLU GLU ILE CYS ARG ARG VAL LYS ASP LEU SEQRES 27 A 339 ASP SEQRES 1 B 352 ALA SER ARG SER GLN ALA GLU ASP VAL ARG VAL GLU GLY SEQRES 2 B 352 SER PHE PRO VAL THR MET LEU PRO GLY ASP GLY VAL GLY SEQRES 3 B 352 PRO GLU LEU MET HIS ALA VAL LYS GLU VAL PHE LYS ALA SEQRES 4 B 352 ALA ALA VAL PRO VAL GLU PHE GLN GLU HIS HIS LEU SER SEQRES 5 B 352 GLU VAL GLN ASN MET ALA SER GLU GLU LYS LEU GLU GLN SEQRES 6 B 352 VAL LEU SER SER MET LYS GLU ASN LYS VAL ALA ILE ILE SEQRES 7 B 352 GLY LYS ILE HIS THR PRO MET GLU TYR LYS GLY GLU LEU SEQRES 8 B 352 ALA SER TYR ASP MET ARG LEU ARG ARG LYS LEU ASP LEU SEQRES 9 B 352 PHE ALA ASN VAL VAL HIS VAL LYS SER LEU PRO GLY TYR SEQRES 10 B 352 MET THR ARG HIS ASN ASN LEU ASP LEU VAL ILE ILE ARG SEQRES 11 B 352 GLU GLN THR GLU GLY GLU TYR SER SER LEU GLU HIS GLU SEQRES 12 B 352 SER ALA ARG GLY VAL ILE GLU CYS LEU LYS ILE VAL THR SEQRES 13 B 352 ARG ALA LYS SER GLN ARG ILE ALA LYS PHE ALA PHE ASP SEQRES 14 B 352 TYR ALA THR LYS LYS GLY ARG GLY LYS VAL THR ALA VAL SEQRES 15 B 352 HIS LYS ALA ASN ILE MET LYS LEU GLY ASP GLY LEU PHE SEQRES 16 B 352 LEU GLN CYS CYS GLU GLU VAL ALA GLU LEU TYR PRO LYS SEQRES 17 B 352 ILE LYS PHE GLU THR MET ILE ILE ASP ASN CYS CYS MET SEQRES 18 B 352 GLN LEU VAL GLN ASN PRO TYR GLN PHE ASP VAL LEU VAL SEQRES 19 B 352 MET PRO ASN LEU TYR GLY ASN ILE ILE ASP ASN LEU ALA SEQRES 20 B 352 ALA GLY LEU VAL GLY GLY ALA GLY VAL VAL PRO GLY GLU SEQRES 21 B 352 SER TYR SER ALA GLU TYR ALA VAL PHE GLU THR GLY ALA SEQRES 22 B 352 ARG HIS PRO PHE ALA GLN ALA VAL GLY ARG ASN ILE ALA SEQRES 23 B 352 ASN PRO THR ALA MET LEU LEU SER ALA SER ASN MET LEU SEQRES 24 B 352 ARG HIS LEU ASN LEU GLU TYR HIS SER SER MET ILE ALA SEQRES 25 B 352 ASP ALA VAL LYS LYS VAL ILE LYS VAL GLY LYS VAL ARG SEQRES 26 B 352 THR SER ASP MET GLY GLY TYR ALA THR CYS HIS ASP PHE SEQRES 27 B 352 THR GLU GLU ILE CYS ARG ARG VAL LYS ASP LEU ASP GLU SEQRES 28 B 352 ASN HET MG A 401 1 HET ADP B 401 27 HETNAM MG MAGNESIUM ION HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 3 MG MG 2+ FORMUL 4 ADP C10 H15 N5 O10 P2 FORMUL 5 HOH *54(H2 O) HELIX 1 AA1 ILE A 15 ALA A 30 1 16 HELIX 2 AA2 PRO A 54 LYS A 65 1 12 HELIX 3 AA3 SER A 82 ASP A 92 1 11 HELIX 4 AA4 GLU A 123 SER A 127 5 5 HELIX 5 AA5 GLU A 146 ASN A 163 1 18 HELIX 6 AA6 MET A 179 SER A 194 1 16 HELIX 7 AA7 LEU A 205 VAL A 213 1 9 HELIX 8 AA8 ASP A 215 PHE A 219 5 5 HELIX 9 AA9 PRO A 225 ILE A 240 1 16 HELIX 10 AB1 GLY A 242 VAL A 245 5 4 HELIX 11 AB2 ALA A 266 ALA A 270 5 5 HELIX 12 AB3 PRO A 277 MET A 291 1 15 HELIX 13 AB4 LEU A 293 GLY A 311 1 19 HELIX 14 AB5 THR A 315 GLY A 319 5 5 HELIX 15 AB6 LYS A 323 LYS A 336 1 14 HELIX 16 AB7 VAL B 25 ALA B 41 1 17 HELIX 17 AB8 ALA B 58 LYS B 74 1 17 HELIX 18 AB9 SER B 93 LEU B 102 1 10 HELIX 19 AC1 GLU B 134 SER B 139 5 6 HELIX 20 AC2 ARG B 157 LYS B 174 1 18 HELIX 21 AC3 LEU B 190 LEU B 205 1 16 HELIX 22 AC4 ILE B 216 ASN B 226 1 11 HELIX 23 AC5 PRO B 227 PHE B 230 5 4 HELIX 24 AC6 PRO B 236 VAL B 251 1 16 HELIX 25 AC7 PHE B 277 VAL B 281 5 5 HELIX 26 AC8 PRO B 288 LEU B 302 1 15 HELIX 27 AC9 LEU B 304 GLY B 322 1 19 HELIX 28 AD1 THR B 326 GLY B 330 5 5 HELIX 29 AD2 THR B 334 ASP B 348 1 15 SHEET 1 AA110 ILE A 34 GLU A 38 0 SHEET 2 AA110 GLN A 5 ILE A 10 1 N GLN A 5 O GLN A 35 SHEET 3 AA110 MET A 66 LYS A 69 1 O LEU A 68 N THR A 8 SHEET 4 AA110 ALA A 257 SER A 261 1 O PHE A 259 N GLY A 67 SHEET 5 AA110 PRO A 247 ILE A 251 -1 N SER A 248 O GLU A 260 SHEET 6 AA110 ALA A 95 VAL A 101 -1 N ALA A 95 O ILE A 251 SHEET 7 AA110 ASN A 114 GLU A 120 -1 O ILE A 115 N CYS A 100 SHEET 8 AA110 VAL A 221 MET A 224 1 O LEU A 222 N ILE A 118 SHEET 9 AA110 ASN A 167 HIS A 172 1 N THR A 169 O VAL A 221 SHEET 10 AA110 LYS A 199 TYR A 204 1 O MET A 203 N ALA A 170 SHEET 1 AA2 4 GLU A 130 VAL A 134 0 SHEET 2 AA2 4 VAL A 137 THR A 145 -1 O ALA A 139 N HIS A 131 SHEET 3 AA2 4 VAL B 148 THR B 156 -1 O CYS B 151 N LYS A 142 SHEET 4 AA2 4 GLU B 141 ALA B 145 -1 N ALA B 145 O VAL B 148 SHEET 1 AA310 GLU B 45 GLU B 48 0 SHEET 2 AA310 PRO B 16 LEU B 20 1 N VAL B 17 O GLN B 47 SHEET 3 AA310 VAL B 75 ILE B 78 1 O ILE B 77 N THR B 18 SHEET 4 AA310 ALA B 267 THR B 271 1 O PHE B 269 N ALA B 76 SHEET 5 AA310 PRO B 258 TYR B 262 -1 N SER B 261 O VAL B 268 SHEET 6 AA310 ALA B 106 LYS B 112 -1 N VAL B 108 O GLU B 260 SHEET 7 AA310 ASP B 125 GLU B 131 -1 O LEU B 126 N VAL B 111 SHEET 8 AA310 VAL B 232 MET B 235 1 O LEU B 233 N ILE B 129 SHEET 9 AA310 LYS B 178 HIS B 183 1 N THR B 180 O VAL B 234 SHEET 10 AA310 LYS B 210 ILE B 215 1 O GLU B 212 N ALA B 181 LINK OD1 ASP A 230 MG MG A 401 1555 1555 2.12 LINK OD1 ASP A 234 MG MG A 401 1555 1555 2.40 LINK MG MG A 401 OD2 ASP B 217 1555 1555 2.07 CRYST1 165.897 165.897 129.583 90.00 90.00 90.00 I 4 2 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 0.006028 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006028 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007717 0.00000