HEADER OXIDOREDUCTASE 16-FEB-12 4AJB
TITLE 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN
TITLE 2 COMPLEX WITH ISOCITRATE, MAGNESIUM(II) AND THIONADP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NADP ISOCITRATE DEHYDROGENASE;
COMPND 3 CHAIN: A;
COMPND 4 EC: 1.1.1.42;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 5 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 4AJB 1 REMARK LINK
REVDAT 1 31-OCT-12 4AJB 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. 1.90 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) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.74
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 64286
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.167
REMARK 3 R VALUE (WORKING SET) : 0.166
REMARK 3 FREE R VALUE : 0.181
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 3235
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 48.7596 - 4.0927 1.00 6474 345 0.1521 0.1549
REMARK 3 2 4.0927 - 3.2487 1.00 6185 335 0.1447 0.1535
REMARK 3 3 3.2487 - 2.8381 1.00 6119 332 0.1684 0.1907
REMARK 3 4 2.8381 - 2.5786 1.00 6106 316 0.1735 0.1986
REMARK 3 5 2.5786 - 2.3938 1.00 6087 303 0.1736 0.2061
REMARK 3 6 2.3938 - 2.2527 1.00 6039 337 0.1716 0.1957
REMARK 3 7 2.2527 - 2.1399 1.00 5995 362 0.1711 0.1800
REMARK 3 8 2.1399 - 2.0467 1.00 6069 291 0.1810 0.1850
REMARK 3 9 2.0467 - 1.9679 1.00 6026 306 0.2048 0.2289
REMARK 3 10 1.9679 - 1.9000 0.99 5951 308 0.2415 0.2626
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 : 0.38
REMARK 3 B_SOL : 51.61
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.420
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.650
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.12010
REMARK 3 B22 (A**2) : -1.12010
REMARK 3 B33 (A**2) : -9.82620
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 : 0.007 3390
REMARK 3 ANGLE : 1.079 4612
REMARK 3 CHIRALITY : 0.073 510
REMARK 3 PLANARITY : 0.005 596
REMARK 3 DIHEDRAL : 14.002 1296
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 4AJB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1290051306.
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 : SLS
REMARK 200 BEAMLINE : X06DA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792
REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL
REMARK 200 CHANNEL CUT CRYSTALS
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64372
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900
REMARK 200 RESOLUTION RANGE LOW (A) : 48.800
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 7.300
REMARK 200 R MERGE (I) : 0.08000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2000
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) : 2.01
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1
REMARK 200 DATA REDUNDANCY IN SHELL : 7.20
REMARK 200 R MERGE FOR SHELL (I) : 0.54000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200
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: 1.85M 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 75.16950
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.52700
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.52700
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.75425
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.52700
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.52700
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.58475
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.52700
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.52700
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.75425
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.52700
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.52700
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.58475
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 75.16950
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: 10690 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 30960 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -82.6 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 O HOH A 2098 O HOH A 2100 1.81
REMARK 500 O HOH A 2010 O HOH A 2032 1.81
REMARK 500 O HOH A 2465 O HOH A 2478 1.82
REMARK 500 O GLN A 80 O HOH A 2126 1.83
REMARK 500 O HOH A 2132 O HOH A 2433 1.84
REMARK 500 O HOH A 2119 O HOH A 2185 1.90
REMARK 500 O HOH A 2011 O HOH A 2032 1.91
REMARK 500 O HOH A 2129 O HOH A 2321 1.95
REMARK 500 O HOH A 2091 O HOH A 2245 1.99
REMARK 500 O HOH A 2414 O HOH A 2489 2.02
REMARK 500 OH TYR A 78 OE1 GLU A 87 2.03
REMARK 500 OE2 GLU A 25 O HOH A 2040 2.07
REMARK 500 O HOH A 2180 O HOH A 2181 2.09
REMARK 500 O HOH A 2030 O HOH A 2065 2.12
REMARK 500 O HOH A 2087 O HOH A 2227 2.17
REMARK 500 O HOH A 2222 O HOH A 2452 2.18
REMARK 500 O HOH A 2096 O HOH A 2257 2.19
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 O HOH A 2166 O HOH A 2488 7555 1.81
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 ARG A 96 -38.19 79.21
REMARK 500 ASP A 148 82.70 -151.60
REMARK 500 GLU A 157 -148.88 -129.19
REMARK 500 ASP A 158 -170.15 68.48
REMARK 500 ASP A 168 -0.81 75.88
REMARK 500 LYS A 230 57.08 -115.67
REMARK 500 THR A 237 -71.30 -114.43
REMARK 500 ASP A 259 -123.54 50.75
REMARK 500 ASP A 259 -125.49 53.74
REMARK 500 ASP A 297 -96.82 -140.31
REMARK 500 ALA A 342 57.59 33.66
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 A2100 DISTANCE = 6.01 ANGSTROMS
REMARK 525 HOH A2230 DISTANCE = 6.14 ANGSTROMS
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 503 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 283 OD2
REMARK 620 2 ASP A 307 OD1 97.8
REMARK 620 3 ICT A 502 O2 159.9 89.3
REMARK 620 4 ICT A 502 O7 89.0 95.7 71.6
REMARK 620 5 HOH A2199 O 104.3 89.3 94.5 165.1
REMARK 620 6 HOH A2393 O 85.1 175.9 88.9 87.2 87.1
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 TAP A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ICT A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 504
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4AJ3 RELATED DB: PDB
REMARK 900 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE IN COMPLEX WITH
REMARK 900 ISOCITRATE, CALCIUM(II) AND NADP - THE PSEUDO-MICHAELIS COMPLEX
REMARK 900 RELATED ID: 4AJA RELATED DB: PDB
REMARK 900 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE IN COMPLEX WITH
REMARK 900 ISOCITRATE, CALCIUM(II) AND THIONADP
REMARK 900 RELATED ID: 4AJC RELATED DB: PDB
REMARK 900 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN
REMARK 900 COMPLEX WITH ALPHA-KETOGLUTARATE, CALCIUM(II ) AND ADENINE
REMARK 900 NUCLEOTIDE PHOSPHATE
DBREF 4AJB A 1 416 UNP P08200 IDH_ECOLI 1 416
SEQADV 4AJB 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 TAP A 501 48
HET ICT A 502 13
HET MG A 503 1
HET SO4 A 504 5
HETNAM TAP 7-THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
HETNAM ICT ISOCITRIC ACID
HETNAM MG MAGNESIUM ION
HETNAM SO4 SULFATE ION
HETSYN TAP TATP
FORMUL 2 TAP C21 H28 N7 O16 P3 S
FORMUL 3 ICT C6 H8 O7
FORMUL 4 MG MG 2+
FORMUL 5 SO4 O4 S 2-
FORMUL 6 HOH *490(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 LEU A 122 1 10
HELIX 5 5 HIS A 143 LEU A 146 5 4
HELIX 6 6 GLU A 157 GLY A 162 5 6
HELIX 7 7 SER A 169 GLU A 182 1 14
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 ALA A 342 ALA A 346 5 5
HELIX 14 14 PRO A 353 MET A 367 1 15
HELIX 15 15 TRP A 369 ALA A 386 1 18
HELIX 16 16 THR A 390 ARG A 395 1 6
HELIX 17 17 LYS A 404 ASN A 415 1 12
SHEET 1 AA 2 THR A 15 GLN A 17 0
SHEET 2 AA 2 LYS A 20 ASN A 22 -1 O LYS A 20 N GLN A 17
SHEET 1 AB12 SER A 64 ILE A 68 0
SHEET 2 AB12 ILE A 28 ILE A 32 1 O ILE A 29 N MET A 66
SHEET 3 AB12 VAL A 97 MET A 100 1 O ILE A 99 N ILE A 32
SHEET 4 AB12 ALA A 333 GLU A 336 1 O ALA A 333 N ALA A 98
SHEET 5 AB12 ALA A 326 ILE A 328 -1 O ASN A 327 N LEU A 334
SHEET 6 AB12 ILE A 126 ARG A 132 -1 O ILE A 126 N ILE A 328
SHEET 7 AB12 ASP A 148 GLU A 154 -1 O MET A 149 N VAL A 131
SHEET 8 AB12 VAL A 298 CYS A 301 1 O ILE A 299 N PHE A 152
SHEET 9 AB12 SER A 224 HIS A 229 1 O SER A 224 N VAL A 298
SHEET 10 AB12 GLU A 274 ILE A 281 1 O VAL A 276 N VAL A 225
SHEET 11 AB12 LEU A 264 LYS A 267 -1 O LEU A 264 N ILE A 277
SHEET 12 AB12 GLU A 256 LEU A 257 -1 O GLU A 256 N LYS A 265
SHEET 1 AC 2 GLU A 164 TRP A 165 0
SHEET 2 AC 2 ILE A 196 GLY A 197 -1 O ILE A 196 N TRP A 165
SHEET 1 AD 2 THR A 388 VAL A 389 0
SHEET 2 AD 2 LYS A 401 LEU A 402 1 O LYS A 401 N VAL A 389
LINK OD2 ASP A 283 MG MG A 503 7555 1555 2.11
LINK OD1 ASP A 307 MG MG A 503 1555 1555 2.07
LINK O2 ICT A 502 MG MG A 503 1555 1555 2.26
LINK O7 ICT A 502 MG MG A 503 1555 1555 2.28
LINK MG MG A 503 O HOH A2199 1555 1555 2.20
LINK MG MG A 503 O HOH A2393 1555 1555 2.21
CISPEP 1 GLY A 261 PRO A 262 0 4.24
SITE 1 AC1 30 LYS A 58 LEU A 103 THR A 105 ARG A 292
SITE 2 AC1 30 THR A 338 HIS A 339 GLY A 340 THR A 341
SITE 3 AC1 30 ALA A 342 TYR A 345 VAL A 351 ASN A 352
SITE 4 AC1 30 TYR A 391 ASP A 392 ARG A 395 ICT A 502
SITE 5 AC1 30 HOH A2167 HOH A2169 HOH A2172 HOH A2182
SITE 6 AC1 30 HOH A2401 HOH A2411 HOH A2412 HOH A2483
SITE 7 AC1 30 HOH A2484 HOH A2485 HOH A2486 HOH A2487
SITE 8 AC1 30 HOH A2488 HOH A2489
SITE 1 AC2 16 SER A 113 ARG A 119 ARG A 129 ARG A 153
SITE 2 AC2 16 TYR A 160 LYS A 230 ASN A 232 ASP A 283
SITE 3 AC2 16 ASP A 307 TAP A 501 MG A 503 HOH A2172
SITE 4 AC2 16 HOH A2182 HOH A2200 HOH A2393 HOH A2484
SITE 1 AC3 5 ASP A 283 ASP A 307 ICT A 502 HOH A2199
SITE 2 AC3 5 HOH A2393
SITE 1 AC4 5 GLY A 108 GLY A 109 GLY A 110 LYS A 235
SITE 2 AC4 5 HOH A2174
CRYST1 103.054 103.054 150.339 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 0.009704 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009704 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006652 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
