HEADER OXIDOREDUCTASE 17-FEB-12 4AJR TITLE 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN TITLE 2 COMPLEX WITH ALPHA-KETOGLUTARATE, MAGNESIUM(II) AND NADPH - THE TITLE 3 PRODUCT COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IDH, IDP, NADP(+)-SPECIFIC ICDH, OXALOSUCCINATE COMPND 5 DECARBOXYLASE; COMPND 6 EC: 1.1.1.42; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE, OXIDATIVE BETA-DECARBOXYLATION EXPDTA X-RAY DIFFRACTION AUTHOR S.GONCALVES,S.P.MILLER,M.A.CARRONDO,A.M.DEAN,P.M.MATIAS REVDAT 2 20-DEC-23 4AJR 1 REMARK LINK REVDAT 1 31-OCT-12 4AJR 0 JRNL AUTH S.GONCALVES,S.P.MILLER,M.A.CARRONDO,A.M.DEAN,P.M.MATIAS JRNL TITL INDUCED FIT AND THE CATALYTIC MECHANISM OF ISOCITRATE JRNL TITL 2 DEHYDROGENASE. JRNL REF BIOCHEMISTRY V. 51 7098 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22891681 JRNL DOI 10.1021/BI300483W REMARK 2 REMARK 2 RESOLUTION. 2.69 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.69 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 23554 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1195 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 52.9042 - 5.5879 1.00 2686 132 0.1754 0.2007 REMARK 3 2 5.5879 - 4.4360 1.00 2523 135 0.1379 0.1846 REMARK 3 3 4.4360 - 3.8755 1.00 2502 141 0.1311 0.1815 REMARK 3 4 3.8755 - 3.5212 1.00 2461 140 0.1431 0.1899 REMARK 3 5 3.5212 - 3.2689 1.00 2483 127 0.1542 0.2155 REMARK 3 6 3.2689 - 3.0762 1.00 2463 139 0.1702 0.2463 REMARK 3 7 3.0762 - 2.9221 1.00 2450 122 0.1919 0.2493 REMARK 3 8 2.9221 - 2.7949 1.00 2429 140 0.2013 0.2522 REMARK 3 9 2.7949 - 2.6873 0.96 2362 119 0.2269 0.2921 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 27.03 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.660 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 22.81210 REMARK 3 B22 (A**2) : 22.81210 REMARK 3 B33 (A**2) : 13.92550 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 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 : 0.008 3349 REMARK 3 ANGLE : 1.139 4543 REMARK 3 CHIRALITY : 0.069 503 REMARK 3 PLANARITY : 0.004 582 REMARK 3 DIHEDRAL : 17.288 1264 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 4AJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1290051346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9535 REMARK 200 MONOCHROMATOR : CHANNEL-CUT ESRF MONOCHROMATOR REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 0.84000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 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 1AI2 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.85 M NH4SO4, 50 MM CITRIC REMARK 280 ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT 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 72.74400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.89400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.89400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.11600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.89400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.89400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.37200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.89400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.89400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.11600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.89400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.89400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.37200 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 72.74400 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: 12200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.7 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 100 TO MET 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 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 OH TYR A 78 OE1 GLU A 87 2.13 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 LEU A 16 77.05 -119.87 REMARK 500 ASN A 18 -117.64 78.61 REMARK 500 LYS A 58 43.39 39.37 REMARK 500 ASP A 81 -17.46 79.78 REMARK 500 ARG A 96 -36.47 74.54 REMARK 500 GLU A 157 -151.03 -130.54 REMARK 500 ASP A 158 -179.35 74.46 REMARK 500 LYS A 230 54.38 -119.32 REMARK 500 MET A 234 74.48 -104.91 REMARK 500 THR A 237 -74.38 -117.83 REMARK 500 ASP A 259 -122.30 58.38 REMARK 500 ASP A 297 -96.21 -137.47 REMARK 500 ALA A 342 70.11 19.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP): REMARK 600 THIS IS NADPH, THE REDUCED FORM OF NADP REMARK 600 RIBOSYLNICOTINAMIDE-5'-PHOSPHATE (NMP): THIS IS A NADP REMARK 600 FRAGMENT FROM HYDROLYSIS 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 A1419 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 283 OD2 REMARK 620 2 ASP A 307 OD1 98.6 REMARK 620 3 AKG A1418 O2 148.6 83.0 REMARK 620 4 AKG A1418 O5 87.6 78.5 61.9 REMARK 620 5 HOH A2051 O 122.0 74.2 88.7 141.9 REMARK 620 6 HOH A2106 O 84.4 162.4 103.5 119.1 89.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 1417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 1418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1419 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AI2 RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND REMARK 900 CALCIUM (FLASH-COOLED) REMARK 900 RELATED ID: 1AI3 RELATED DB: PDB REMARK 900 ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL REMARK 900 STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES REMARK 900 RELATED ID: 1BL5 RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE REMARK 900 STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION REMARK 900 RELATED ID: 1CW1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO REMARK 900 ISOCITRATE AND MN2+ REMARK 900 RELATED ID: 1CW4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH REMARK 900 ALPHA- KETOGLUTARATE REMARK 900 RELATED ID: 1CW7 RELATED DB: PDB REMARK 900 LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG- REMARK 900 ISOCITRATE REMARK 900 RELATED ID: 1GRO RELATED DB: PDB REMARK 900 RELATED ID: 1GRP RELATED DB: PDB REMARK 900 RELATED ID: 1HJ6 RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH REMARK 900 ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED) REMARK 900 RELATED ID: 1IDC RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE REMARK 900 INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY REMARK 900 RELATED ID: 1IDD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME REMARK 900 RELATED ID: 1IDE RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE REMARK 900 COMPLEX (LAUE DETERMINATION) REMARK 900 RELATED ID: 1IDF RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME REMARK 900 RELATED ID: 1IKA RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ALPHA-KETOGLUTARATE REMARK 900 RELATED ID: 1ISO RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP + --> NAD+ REMARK 900 SPECIFICITY-REVERSAL MUTANT REMARK 900 RELATED ID: 1P8F RELATED DB: PDB REMARK 900 A FOUR LOCATION MODEL TO EXPLAIN THE STEREOSPECIFICITY OFPROTEINS. REMARK 900 RELATED ID: 1PB1 RELATED DB: PDB REMARK 900 A FOUR LOCATION MODEL TO EXPLAIN THE STEREOSPECIFICITY OFPROTEINS. REMARK 900 RELATED ID: 1PB3 RELATED DB: PDB REMARK 900 SITES OF BINDING AND ORIENTATION IN A FOUR LOCATION MODELFOR REMARK 900 PROTEIN STEREOSPECIFICITY. REMARK 900 RELATED ID: 1SJS RELATED DB: PDB REMARK 900 ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY REMARK 900 DOMAIN SHIFTING REMARK 900 RELATED ID: 3ICD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE REMARK 900 RELATED ID: 4ICD RELATED DB: PDB REMARK 900 PHOSPHORYLATED ISOCITRATE DEHYDROGENASE REMARK 900 RELATED ID: 5ICD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEX WITH MG2+ AND ISOCITRATE REMARK 900 RELATED ID: 6ICD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE (MUTANT WITH SER 113 REPLACED BY ASP) REMARK 900 (S113D) REMARK 900 RELATED ID: 7ICD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE (MUTANT WITH SER 113 REPLACED BY GLU) (/ REMARK 900 S113E) REMARK 900 RELATED ID: 8ICD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE (MUTANT WITH SER 113 REPLACED BY GLU) REMARK 900 (S113E) COMPLEX WITH MG2+ AND ISOCITRATE REMARK 900 RELATED ID: 9ICD RELATED DB: PDB REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEX WITH NADP+ DBREF 4AJR A 1 416 UNP P08200 IDH_ECOLI 1 416 SEQADV 4AJR MET A 100 UNP P08200 LYS 100 ENGINEERED MUTATION 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 MET 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 NMN A 504 22 HET NAP A1417 48 HET AKG A1418 10 HET MG A1419 1 HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM AKG 2-OXOGLUTARIC ACID HETNAM MG MAGNESIUM ION HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE FORMUL 2 NMN C11 H16 N2 O8 P 1+ FORMUL 3 NAP C21 H28 N7 O17 P3 FORMUL 4 AKG C5 H6 O5 FORMUL 5 MG MG 2+ FORMUL 6 HOH *127(H2 O) HELIX 1 1 ILE A 37 LYS A 58 1 22 HELIX 2 2 GLY A 71 GLY A 79 1 9 HELIX 3 3 PRO A 85 ARG A 96 1 12 HELIX 4 4 SER A 113 ASP A 123 1 11 HELIX 5 5 HIS A 143 LEU A 146 5 4 HELIX 6 6 ASP A 158 GLY A 162 5 5 HELIX 7 7 SER A 169 MET A 183 1 15 HELIX 8 8 SER A 202 ASN A 220 1 19 HELIX 9 9 THR A 237 GLY A 254 1 18 HELIX 10 10 ALA A 282 ARG A 292 1 11 HELIX 11 11 PRO A 293 TYR A 296 5 4 HELIX 12 12 MET A 302 VAL A 317 1 16 HELIX 13 13 GLY A 319 ILE A 322 5 4 HELIX 14 14 ALA A 342 ALA A 346 5 5 HELIX 15 15 PRO A 353 MET A 367 1 15 HELIX 16 16 TRP A 369 ALA A 386 1 18 HELIX 17 17 THR A 390 ARG A 395 1 6 HELIX 18 18 LYS A 404 ASN A 415 1 12 SHEET 1 AA12 SER A 64 GLU A 67 0 SHEET 2 AA12 ILE A 28 ILE A 32 1 O ILE A 29 N MET A 66 SHEET 3 AA12 VAL A 97 MET A 100 1 O ILE A 99 N ILE A 32 SHEET 4 AA12 ALA A 333 ALA A 337 1 O ALA A 333 N ALA A 98 SHEET 5 AA12 PRO A 324 ILE A 328 -1 O GLY A 325 N GLU A 336 SHEET 6 AA12 ILE A 126 ARG A 132 -1 O ILE A 126 N ILE A 328 SHEET 7 AA12 ASP A 148 GLU A 154 -1 O MET A 149 N VAL A 131 SHEET 8 AA12 VAL A 298 CYS A 301 1 O ILE A 299 N PHE A 152 SHEET 9 AA12 SER A 224 HIS A 229 1 O SER A 224 N VAL A 298 SHEET 10 AA12 GLU A 274 ILE A 281 1 O VAL A 276 N VAL A 225 SHEET 11 AA12 LEU A 264 LYS A 267 -1 O LEU A 264 N ILE A 277 SHEET 12 AA12 GLU A 256 LEU A 257 -1 O GLU A 256 N LYS A 265 SHEET 1 AB 2 GLU A 164 TRP A 165 0 SHEET 2 AB 2 ILE A 196 GLY A 197 -1 O ILE A 196 N TRP A 165 SHEET 1 AC 2 THR A 388 VAL A 389 0 SHEET 2 AC 2 LYS A 401 LEU A 402 1 O LYS A 401 N VAL A 389 LINK OD2 ASP A 283 MG MG A1419 7555 1555 2.58 LINK OD1 ASP A 307 MG MG A1419 1555 1555 2.35 LINK O2 AKG A1418 MG MG A1419 1555 1555 2.81 LINK O5 AKG A1418 MG MG A1419 1555 1555 2.80 LINK MG MG A1419 O HOH A2051 1555 1555 2.72 LINK MG MG A1419 O HOH A2106 1555 1555 2.50 CISPEP 1 GLY A 261 PRO A 262 0 1.41 SITE 1 AC1 4 ILE A 258 GLY A 261 PRO A 262 TRP A 263 SITE 1 AC2 34 ILE A 37 PRO A 102 LEU A 103 THR A 104 SITE 2 AC2 34 THR A 105 ASN A 115 ASN A 232 ILE A 281 SITE 3 AC2 34 GLN A 288 ARG A 292 ILE A 320 GLY A 321 SITE 4 AC2 34 GLU A 336 THR A 338 HIS A 339 GLY A 340 SITE 5 AC2 34 THR A 341 ALA A 342 LYS A 344 TYR A 345 SITE 6 AC2 34 VAL A 351 ASN A 352 TYR A 391 ASP A 392 SITE 7 AC2 34 AKG A1418 HOH A2044 HOH A2100 HOH A2102 SITE 8 AC2 34 HOH A2103 HOH A2107 HOH A2124 HOH A2125 SITE 9 AC2 34 HOH A2126 HOH A2127 SITE 1 AC3 14 THR A 105 SER A 113 ASN A 115 ARG A 119 SITE 2 AC3 14 ARG A 129 ARG A 153 TYR A 160 LYS A 230 SITE 3 AC3 14 ASP A 307 THR A 338 NAP A1417 MG A1419 SITE 4 AC3 14 HOH A2044 HOH A2094 SITE 1 AC4 6 ASP A 283 ASP A 307 ASP A 311 AKG A1418 SITE 2 AC4 6 HOH A2051 HOH A2106 CRYST1 105.788 105.788 145.488 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 0.009453 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009453 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006873 0.00000