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- PDB-1ak5: INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH) FROM TRITRICHOMONAS FOETUS -

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Basic information

Entry
Database: PDB / ID: 1ak5
TitleINOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH) FROM TRITRICHOMONAS FOETUS
ComponentsINOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / DEHYDROGENASE / ALPHA-8-BETA-8 BARREL / TIM BARREL / PURINE METABOLISM / TETRAMER / C4-TETRAMER
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / protein-containing complex / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesTritrichomonas foetus (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsWhitby, F.G.
CitationJournal: Biochemistry / Year: 1997
Title: Crystal structure of Tritrichomonas foetus inosine-5'-monophosphate dehydrogenase and the enzyme-product complex.
Authors: Whitby, F.G. / Luecke, H. / Kuhn, P. / Somoza, J.R. / Huete-Perez, J.A. / Phillips, J.D. / Hill, C.P. / Fletterick, R.J. / Wang, C.C.
History
DepositionMay 28, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6362
Polymers55,5401
Non-polymers961
Water1,02757
1
A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules

A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)222,5448
Polymers222,1604
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation15_565y,-x+1,z1
crystal symmetry operation16_655-y+1,x,z1
Buried area9520 Å2
ΔGint-129 kcal/mol
Surface area50500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)157.250, 157.250, 157.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

#1: Protein INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE / IMPDH


Mass: 55540.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DISULFIDE LINKAGE 26-459 / Source: (gene. exp.) Tritrichomonas foetus (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: P50097, IMP dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.4 / Details: 2.2M AS, 2% PEG-550-MME, pH 7.4
Crystal grow
*PLUS
Method: hanging, sitting drop, liquid diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-97 mg/mlprotein1drop
22.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 153931 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057
Reflection shell
*PLUS
Rmerge(I) obs: 0.25

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATA/AGROVATAdata reduction
PHASESphasing
XTALVIEWrefinement
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2.3→8 Å / Rfactor Rfree error: 0 / Data cutoff high absF: 100000000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2945 10 %RANDOM
Rwork0.218 ---
obs0.218 28851 97.8 %-
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 5 57 2582
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.593
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.339 347 10 %
Rwork0.3 3043 -
obs--96 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.3

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