HEADER OXIDOREDUCTASE 02-JUL-10 3NT5
TITLE CRYSTAL STRUCTURE OF MYO-INOSITOL DEHYDROGENASE FROM BACILLUS SUBTILIS
TITLE 2 WITH BOUND COFACTOR AND PRODUCT INOSOSE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3-DEHYDROGENASE;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: MYO-INOSITOL 2-DEHYDROGENASE/D-CHIRO-INOSITOL 3-
COMPND 5 DEHYDROGENASE, MI 2-DEHYDROGENASE/DCI 3-DEHYDROGENASE;
COMPND 6 EC: 1.1.1.18;
COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS;
SOURCE 3 ORGANISM_TAXID: 1423;
SOURCE 4 GENE: BSU39700, E83G, IDH, IOLG, NP_391849.2;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PHISTEV
KEYWDS BSIDH, OXIDOREDUCTASE, N-TERMINAL ROSSMANN FOLD DOMAIN,
KEYWDS 2 GLYCERALDEHYDE-3-PHOSPHATE LIKE C-TERMINAL DOMAIN, NAD(H), INOSITOL,
KEYWDS 3 INOSOSE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.E.VAN STRAATEN,D.R.J.PALMER,D.A.R.SANDERS
REVDAT 4 06-SEP-23 3NT5 1 REMARK HETSYN
REVDAT 3 08-NOV-17 3NT5 1 REMARK
REVDAT 2 01-DEC-10 3NT5 1 JRNL
REVDAT 1 15-SEP-10 3NT5 0
JRNL AUTH K.E.VAN STRAATEN,H.ZHENG,D.R.PALMER,D.A.SANDERS
JRNL TITL STRUCTURAL INVESTIGATION OF MYO-INOSITOL DEHYDROGENASE FROM
JRNL TITL 2 BACILLUS SUBTILIS: IMPLICATIONS FOR CATALYTIC MECHANISM AND
JRNL TITL 3 INOSITOL DEHYDROGENASE SUBFAMILY CLASSIFICATION.
JRNL REF BIOCHEM.J. V. 432 237 2010
JRNL REFN ISSN 0264-6021
JRNL PMID 20809899
JRNL DOI 10.1042/BJ20101079
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.5_2
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) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.12
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9
REMARK 3 NUMBER OF REFLECTIONS : 22866
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.243
REMARK 3 R VALUE (WORKING SET) : 0.241
REMARK 3 FREE R VALUE : 0.291
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.120
REMARK 3 FREE R VALUE TEST SET COUNT : 1170
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 39.1254 - 5.7958 1.00 2802 156 0.2008 0.2698
REMARK 3 2 5.7958 - 4.6026 1.00 2725 140 0.2048 0.2371
REMARK 3 3 4.6026 - 4.0215 1.00 2711 162 0.2257 0.2599
REMARK 3 4 4.0215 - 3.6541 1.00 2706 133 0.2788 0.3449
REMARK 3 5 3.6541 - 3.3923 1.00 2690 142 0.3073 0.3609
REMARK 3 6 3.3923 - 3.1924 1.00 2698 150 0.3078 0.3590
REMARK 3 7 3.1924 - 3.0326 1.00 2690 140 0.3279 0.3335
REMARK 3 8 3.0326 - 2.9006 1.00 2674 147 0.3185 0.3418
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 : 0.31
REMARK 3 B_SOL : 79.12
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.980
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 80.00
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 111.7
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
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 : 0.010 5494
REMARK 3 ANGLE : 1.335 7470
REMARK 3 CHIRALITY : 0.080 844
REMARK 3 PLANARITY : 0.005 950
REMARK 3 DIHEDRAL : 20.076 2128
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 : 4
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 1:40 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 SELECTION : CHAIN 'B' AND (RESSEQ 1:40 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 ATOM PAIRS NUMBER : 291
REMARK 3 RMSD : 0.038
REMARK 3 NCS GROUP : 2
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 48:74 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 SELECTION : CHAIN 'B' AND (RESSEQ 48:74 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 ATOM PAIRS NUMBER : 206
REMARK 3 RMSD : 0.033
REMARK 3 NCS GROUP : 3
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 76:117 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 SELECTION : CHAIN 'B' AND (RESSEQ 76:117 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 ATOM PAIRS NUMBER : 317
REMARK 3 RMSD : 0.037
REMARK 3 NCS GROUP : 4
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: CHAIN 'A' AND (RESSEQ 120:337 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 SELECTION : CHAIN 'B' AND (RESSEQ 120:337 ) AND (NOT
REMARK 3 ELEMENT H) AND (NOT ELEMENT D)
REMARK 3 ATOM PAIRS NUMBER : 1737
REMARK 3 RMSD : 0.039
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 3NT5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-10.
REMARK 100 THE DEPOSITION ID IS D_1000060247.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 21-MAR-09
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.4
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : CLSI
REMARK 200 BEAMLINE : 08ID-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934
REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK
REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.9.8.0L
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25421
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
REMARK 200 RESOLUTION RANGE LOW (A) : 39.122
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 22.38
REMARK 200 R MERGE (I) : 0.13000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 22.80
REMARK 200 R MERGE FOR SHELL (I) : 0.90500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 3MZ0 (APO-IDH)
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 63.31
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.35
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRI-SODIUM CITRATE PH 5.4, 2.6M
REMARK 280 AMMONIUM SULFATE, MICROBATCH, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 3
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290 5555 Z,X,Y
REMARK 290 6555 Z+1/2,-X+1/2,-Y
REMARK 290 7555 -Z+1/2,-X,Y+1/2
REMARK 290 8555 -Z,X+1/2,-Y+1/2
REMARK 290 9555 Y,Z,X
REMARK 290 10555 -Y,Z+1/2,-X+1/2
REMARK 290 11555 Y+1/2,-Z+1/2,-X
REMARK 290 12555 -Y+1/2,-Z,X+1/2
REMARK 290 13555 X+1/2,Y+1/2,Z+1/2
REMARK 290 14555 -X,-Y+1/2,Z
REMARK 290 15555 -X+1/2,Y,-Z
REMARK 290 16555 X,-Y,-Z+1/2
REMARK 290 17555 Z+1/2,X+1/2,Y+1/2
REMARK 290 18555 Z,-X,-Y+1/2
REMARK 290 19555 -Z,-X+1/2,Y
REMARK 290 20555 -Z+1/2,X,-Y
REMARK 290 21555 Y+1/2,Z+1/2,X+1/2
REMARK 290 22555 -Y+1/2,Z,-X
REMARK 290 23555 Y,-Z,-X+1/2
REMARK 290 24555 -Y,-Z+1/2,X
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 91.74900
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.74900
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 91.74900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 91.74900
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 91.74900
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 91.74900
REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 91.74900
REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 91.74900
REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 91.74900
REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 91.74900
REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 91.74900
REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 91.74900
REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 91.74900
REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 91.74900
REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 91.74900
REMARK 290 SMTRY1 14 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 91.74900
REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 15 -1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY2 15 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 16 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 16 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 91.74900
REMARK 290 SMTRY1 17 0.000000 0.000000 1.000000 91.74900
REMARK 290 SMTRY2 17 1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY3 17 0.000000 1.000000 0.000000 91.74900
REMARK 290 SMTRY1 18 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY2 18 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 18 0.000000 -1.000000 0.000000 91.74900
REMARK 290 SMTRY1 19 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY2 19 -1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY3 19 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY1 20 0.000000 0.000000 -1.000000 91.74900
REMARK 290 SMTRY2 20 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 20 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY1 21 0.000000 1.000000 0.000000 91.74900
REMARK 290 SMTRY2 21 0.000000 0.000000 1.000000 91.74900
REMARK 290 SMTRY3 21 1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY1 22 0.000000 -1.000000 0.000000 91.74900
REMARK 290 SMTRY2 22 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY3 22 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY1 23 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 23 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY3 23 -1.000000 0.000000 0.000000 91.74900
REMARK 290 SMTRY1 24 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 24 0.000000 0.000000 -1.000000 91.74900
REMARK 290 SMTRY3 24 1.000000 0.000000 0.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 16700 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 50260 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -91.74900
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 17230 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 83220 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -100.0 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 350 BIOMT1 2 0.000000 0.000000 -1.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 91.74900
REMARK 350 BIOMT3 2 0.000000 -1.000000 0.000000 91.74900
REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 -91.74900
REMARK 350 BIOMT2 3 0.000000 0.000000 -1.000000 91.74900
REMARK 350 BIOMT3 3 -1.000000 0.000000 0.000000 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 SER A 338
REMARK 465 PHE A 339
REMARK 465 THR A 340
REMARK 465 THR A 341
REMARK 465 VAL A 342
REMARK 465 GLN A 343
REMARK 465 ASN A 344
REMARK 465 SER B 338
REMARK 465 PHE B 339
REMARK 465 THR B 340
REMARK 465 THR B 341
REMARK 465 VAL B 342
REMARK 465 GLN B 343
REMARK 465 ASN B 344
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 NE2 HIS B 176 O2 ISE B 345 2.12
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 THR A 10 43.01 -88.01
REMARK 500 ALA A 32 126.18 177.83
REMARK 500 VAL A 45 -37.96 -39.63
REMARK 500 GLN A 47 -51.99 -27.46
REMARK 500 GLN A 49 58.44 34.34
REMARK 500 ASN A 51 70.14 -116.30
REMARK 500 ALA A 63 -70.46 -48.20
REMARK 500 ASP A 64 138.19 -28.79
REMARK 500 THR A 73 53.05 -141.87
REMARK 500 VAL A 116 20.95 -62.60
REMARK 500 VAL A 144 -54.84 -25.11
REMARK 500 THR A 166 -9.81 -46.77
REMARK 500 GLU A 190 -71.75 -79.85
REMARK 500 GLN A 193 146.50 -170.54
REMARK 500 LYS A 198 105.03 -42.05
REMARK 500 LYS A 232 -37.03 72.68
REMARK 500 ILE A 288 -75.93 -53.87
REMARK 500 LYS A 294 -13.02 -162.70
REMARK 500 GLU A 331 135.00 -38.91
REMARK 500 THR B 10 44.07 -84.29
REMARK 500 ALA B 32 124.40 175.10
REMARK 500 GLN B 49 58.98 31.38
REMARK 500 ASN B 51 68.55 -114.58
REMARK 500 ALA B 63 -70.78 -47.54
REMARK 500 ASP B 64 136.43 -27.69
REMARK 500 THR B 73 51.62 -143.53
REMARK 500 TRP B 75 134.39 -38.49
REMARK 500 VAL B 116 21.05 -62.67
REMARK 500 HIS B 143 -0.26 72.73
REMARK 500 VAL B 144 -54.56 -25.10
REMARK 500 LEU B 149 -50.32 -123.10
REMARK 500 THR B 166 -6.57 -47.77
REMARK 500 THR B 173 -60.49 -100.11
REMARK 500 GLU B 190 -72.69 -77.88
REMARK 500 LYS B 198 107.89 -42.18
REMARK 500 LYS B 232 -34.79 72.60
REMARK 500 ILE B 288 -75.67 -55.86
REMARK 500 LYS B 294 -14.96 -160.14
REMARK 500 GLU B 331 135.55 -36.78
REMARK 500 PHE B 335 -51.85 -28.55
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 NAD A 400
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAI B 400
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ISE A 345
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ISE B 345
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3MZ0 RELATED DB: PDB
REMARK 900 APO-IDH
REMARK 900 RELATED ID: 3NT2 RELATED DB: PDB
REMARK 900 HOLO-IDH IDH WITH BOUND COFACTOR NAD(H)
REMARK 900 RELATED ID: 3NT4 RELATED DB: PDB
REMARK 900 IDH WITH BOUND COFACTOR AND INOSITOL
REMARK 900 RELATED ID: 3NTQ RELATED DB: PDB
REMARK 900 K97V MUTANT IDH WITH BOUND COFACTOR
REMARK 900 RELATED ID: 3NTR RELATED DB: PDB
REMARK 900 K97V MUTANT IDH WITH BOUND COFACTOR AND INOSITOL
DBREF 3NT5 A 1 344 UNP P26935 IOLG_BACSU 1 344
DBREF 3NT5 B 1 344 UNP P26935 IOLG_BACSU 1 344
SEQRES 1 A 344 MET SER LEU ARG ILE GLY VAL ILE GLY THR GLY ALA ILE
SEQRES 2 A 344 GLY LYS GLU HIS ILE ASN ARG ILE THR ASN LYS LEU SER
SEQRES 3 A 344 GLY ALA GLU ILE VAL ALA VAL THR ASP VAL ASN GLN GLU
SEQRES 4 A 344 ALA ALA GLN LYS VAL VAL GLU GLN TYR GLN LEU ASN ALA
SEQRES 5 A 344 THR VAL TYR PRO ASN ASP ASP SER LEU LEU ALA ASP GLU
SEQRES 6 A 344 ASN VAL ASP ALA VAL LEU VAL THR SER TRP GLY PRO ALA
SEQRES 7 A 344 HIS GLU SER SER VAL LEU LYS ALA ILE LYS ALA GLN LYS
SEQRES 8 A 344 TYR VAL PHE CYS GLU LYS PRO LEU ALA THR THR ALA GLU
SEQRES 9 A 344 GLY CYS MET ARG ILE VAL GLU GLU GLU ILE LYS VAL GLY
SEQRES 10 A 344 LYS ARG LEU VAL GLN VAL GLY PHE MET ARG ARG TYR ASP
SEQRES 11 A 344 SER GLY TYR VAL GLN LEU LYS GLU ALA LEU ASP ASN HIS
SEQRES 12 A 344 VAL ILE GLY GLU PRO LEU MET ILE HIS CYS ALA HIS ARG
SEQRES 13 A 344 ASN PRO THR VAL GLY ASP ASN TYR THR THR ASP MET ALA
SEQRES 14 A 344 VAL VAL ASP THR LEU VAL HIS GLU ILE ASP VAL LEU HIS
SEQRES 15 A 344 TRP LEU VAL ASN ASP ASP TYR GLU SER VAL GLN VAL ILE
SEQRES 16 A 344 TYR PRO LYS LYS SER LYS ASN ALA LEU PRO HIS LEU LYS
SEQRES 17 A 344 ASP PRO GLN ILE VAL VAL ILE GLU THR LYS GLY GLY ILE
SEQRES 18 A 344 VAL ILE ASN ALA GLU ILE TYR VAL ASN CYS LYS TYR GLY
SEQRES 19 A 344 TYR ASP ILE GLN CYS GLU ILE VAL GLY GLU ASP GLY ILE
SEQRES 20 A 344 ILE LYS LEU PRO GLU PRO SER SER ILE SER LEU ARG LYS
SEQRES 21 A 344 GLU GLY ARG PHE SER THR ASP ILE LEU MET ASP TRP GLN
SEQRES 22 A 344 ARG ARG PHE VAL ALA ALA TYR ASP VAL GLU ILE GLN ASP
SEQRES 23 A 344 PHE ILE ASP SER ILE GLN LYS LYS GLY GLU VAL SER GLY
SEQRES 24 A 344 PRO THR ALA TRP ASP GLY TYR ILE ALA ALA VAL THR THR
SEQRES 25 A 344 ASP ALA CYS VAL LYS ALA GLN GLU SER GLY GLN LYS GLU
SEQRES 26 A 344 LYS VAL GLU LEU LYS GLU LYS PRO GLU PHE TYR GLN SER
SEQRES 27 A 344 PHE THR THR VAL GLN ASN
SEQRES 1 B 344 MET SER LEU ARG ILE GLY VAL ILE GLY THR GLY ALA ILE
SEQRES 2 B 344 GLY LYS GLU HIS ILE ASN ARG ILE THR ASN LYS LEU SER
SEQRES 3 B 344 GLY ALA GLU ILE VAL ALA VAL THR ASP VAL ASN GLN GLU
SEQRES 4 B 344 ALA ALA GLN LYS VAL VAL GLU GLN TYR GLN LEU ASN ALA
SEQRES 5 B 344 THR VAL TYR PRO ASN ASP ASP SER LEU LEU ALA ASP GLU
SEQRES 6 B 344 ASN VAL ASP ALA VAL LEU VAL THR SER TRP GLY PRO ALA
SEQRES 7 B 344 HIS GLU SER SER VAL LEU LYS ALA ILE LYS ALA GLN LYS
SEQRES 8 B 344 TYR VAL PHE CYS GLU LYS PRO LEU ALA THR THR ALA GLU
SEQRES 9 B 344 GLY CYS MET ARG ILE VAL GLU GLU GLU ILE LYS VAL GLY
SEQRES 10 B 344 LYS ARG LEU VAL GLN VAL GLY PHE MET ARG ARG TYR ASP
SEQRES 11 B 344 SER GLY TYR VAL GLN LEU LYS GLU ALA LEU ASP ASN HIS
SEQRES 12 B 344 VAL ILE GLY GLU PRO LEU MET ILE HIS CYS ALA HIS ARG
SEQRES 13 B 344 ASN PRO THR VAL GLY ASP ASN TYR THR THR ASP MET ALA
SEQRES 14 B 344 VAL VAL ASP THR LEU VAL HIS GLU ILE ASP VAL LEU HIS
SEQRES 15 B 344 TRP LEU VAL ASN ASP ASP TYR GLU SER VAL GLN VAL ILE
SEQRES 16 B 344 TYR PRO LYS LYS SER LYS ASN ALA LEU PRO HIS LEU LYS
SEQRES 17 B 344 ASP PRO GLN ILE VAL VAL ILE GLU THR LYS GLY GLY ILE
SEQRES 18 B 344 VAL ILE ASN ALA GLU ILE TYR VAL ASN CYS LYS TYR GLY
SEQRES 19 B 344 TYR ASP ILE GLN CYS GLU ILE VAL GLY GLU ASP GLY ILE
SEQRES 20 B 344 ILE LYS LEU PRO GLU PRO SER SER ILE SER LEU ARG LYS
SEQRES 21 B 344 GLU GLY ARG PHE SER THR ASP ILE LEU MET ASP TRP GLN
SEQRES 22 B 344 ARG ARG PHE VAL ALA ALA TYR ASP VAL GLU ILE GLN ASP
SEQRES 23 B 344 PHE ILE ASP SER ILE GLN LYS LYS GLY GLU VAL SER GLY
SEQRES 24 B 344 PRO THR ALA TRP ASP GLY TYR ILE ALA ALA VAL THR THR
SEQRES 25 B 344 ASP ALA CYS VAL LYS ALA GLN GLU SER GLY GLN LYS GLU
SEQRES 26 B 344 LYS VAL GLU LEU LYS GLU LYS PRO GLU PHE TYR GLN SER
SEQRES 27 B 344 PHE THR THR VAL GLN ASN
HET NAD A 400 44
HET ISE A 345 12
HET NAI B 400 44
HET ISE B 345 12
HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE
HETNAM ISE (2R,3S,4S,5R,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXANONE
HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
HETSYN ISE INOSOSE; MYO-INOSOSE
HETSYN NAI NADH
FORMUL 3 NAD C21 H27 N7 O14 P2
FORMUL 4 ISE 2(C6 H10 O6)
FORMUL 5 NAI C21 H29 N7 O14 P2
HELIX 1 1 GLY A 11 LYS A 24 1 14
HELIX 2 2 ASN A 37 TYR A 48 1 12
HELIX 3 3 ASN A 57 ASP A 64 1 8
HELIX 4 4 TRP A 75 PRO A 77 5 3
HELIX 5 5 ALA A 78 ALA A 89 1 12
HELIX 6 6 THR A 102 VAL A 116 1 15
HELIX 7 7 PHE A 125 TYR A 129 5 5
HELIX 8 8 ASP A 130 ASN A 142 1 13
HELIX 9 9 ASP A 167 ASP A 172 1 6
HELIX 10 10 LEU A 174 ASN A 186 1 13
HELIX 11 11 ASP A 271 PHE A 276 1 6
HELIX 12 12 PHE A 276 LYS A 293 1 18
HELIX 13 13 THR A 301 GLY A 322 1 22
HELIX 14 14 GLY B 11 LYS B 24 1 14
HELIX 15 15 ASN B 37 TYR B 48 1 12
HELIX 16 16 ASN B 57 ASP B 64 1 8
HELIX 17 17 TRP B 75 PRO B 77 5 3
HELIX 18 18 ALA B 78 ALA B 89 1 12
HELIX 19 19 THR B 102 VAL B 116 1 15
HELIX 20 20 PHE B 125 TYR B 129 5 5
HELIX 21 21 ASP B 130 ASN B 142 1 13
HELIX 22 22 ASP B 167 ASP B 172 1 6
HELIX 23 23 LEU B 174 ASN B 186 1 13
HELIX 24 24 ASP B 271 LYS B 293 1 23
HELIX 25 25 THR B 301 GLY B 322 1 22
SHEET 1 A 6 THR A 53 VAL A 54 0
SHEET 2 A 6 ALA A 28 THR A 34 1 N VAL A 33 O THR A 53
SHEET 3 A 6 LEU A 3 ILE A 8 1 N VAL A 7 O ALA A 32
SHEET 4 A 6 ALA A 69 VAL A 72 1 O ALA A 69 N GLY A 6
SHEET 5 A 6 TYR A 92 CYS A 95 1 O TYR A 92 N VAL A 70
SHEET 6 A 6 VAL A 121 VAL A 123 1 O GLN A 122 N CYS A 95
SHEET 1 B 6 TYR A 189 ILE A 195 0
SHEET 2 B 6 GLN A 211 THR A 217 -1 O ILE A 212 N ILE A 195
SHEET 3 B 6 VAL A 222 TYR A 228 -1 O ILE A 223 N ILE A 215
SHEET 4 B 6 PRO A 148 ARG A 156 1 N ILE A 151 O ASN A 224
SHEET 5 B 6 ASP A 236 GLY A 243 -1 O GLU A 240 N HIS A 152
SHEET 6 B 6 ILE A 247 LYS A 249 -1 O ILE A 248 N ILE A 241
SHEET 1 C 2 LEU A 258 LYS A 260 0
SHEET 2 C 2 ARG A 263 SER A 265 -1 O SER A 265 N LEU A 258
SHEET 1 D 6 THR B 53 VAL B 54 0
SHEET 2 D 6 ALA B 28 THR B 34 1 N VAL B 33 O THR B 53
SHEET 3 D 6 LEU B 3 ILE B 8 1 N VAL B 7 O ALA B 32
SHEET 4 D 6 ALA B 69 VAL B 72 1 O ALA B 69 N GLY B 6
SHEET 5 D 6 TYR B 92 CYS B 95 1 O TYR B 92 N VAL B 70
SHEET 6 D 6 VAL B 121 VAL B 123 1 O GLN B 122 N CYS B 95
SHEET 1 E 6 TYR B 189 ILE B 195 0
SHEET 2 E 6 GLN B 211 THR B 217 -1 O GLU B 216 N SER B 191
SHEET 3 E 6 VAL B 222 TYR B 228 -1 O ILE B 223 N ILE B 215
SHEET 4 E 6 PRO B 148 ARG B 156 1 N ILE B 151 O ASN B 224
SHEET 5 E 6 ASP B 236 GLY B 243 -1 O GLU B 240 N HIS B 152
SHEET 6 E 6 ILE B 247 LYS B 249 -1 O ILE B 248 N ILE B 241
SHEET 1 F 2 LEU B 258 LYS B 260 0
SHEET 2 F 2 ARG B 263 SER B 265 -1 O SER B 265 N LEU B 258
CISPEP 1 LYS A 97 PRO A 98 0 2.17
CISPEP 2 ASP A 209 PRO A 210 0 0.41
CISPEP 3 LYS B 97 PRO B 98 0 3.32
CISPEP 4 ASP B 209 PRO B 210 0 3.33
SITE 1 AC1 17 GLY A 9 GLY A 11 ALA A 12 ILE A 13
SITE 2 AC1 17 THR A 34 ASP A 35 VAL A 36 GLN A 42
SITE 3 AC1 17 SER A 74 TRP A 75 GLY A 76 ALA A 78
SITE 4 AC1 17 GLU A 96 LYS A 97 GLY A 124 MET A 126
SITE 5 AC1 17 TYR A 280
SITE 1 AC2 12 ALA B 12 ILE B 13 THR B 34 ASP B 35
SITE 2 AC2 12 VAL B 36 SER B 74 TRP B 75 ALA B 78
SITE 3 AC2 12 HIS B 79 LYS B 97 TRP B 272 ISE B 345
SITE 1 AC3 6 LYS A 97 HIS A 155 ASN A 157 ASP A 172
SITE 2 AC3 6 HIS A 176 TYR A 235
SITE 1 AC4 8 LYS B 97 ARG B 127 HIS B 155 ASN B 157
SITE 2 AC4 8 ASP B 172 HIS B 176 TYR B 235 NAI B 400
CRYST1 183.498 183.498 183.498 90.00 90.00 90.00 I 21 3 48
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 0.005450 0.000000 0.000000 0.00000
SCALE2 0.000000 0.005450 0.000000 0.00000
SCALE3 0.000000 0.000000 0.005450 0.00000
(ATOM LINES ARE NOT SHOWN.)
END