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- PDB-1wpw: Crystal Structure of IPMDH from Sulfolobus tokodaii -

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Basic information

Entry
Database: PDB / ID: 1wpw
TitleCrystal Structure of IPMDH from Sulfolobus tokodaii
Components3-isopropylmalate dehydrogenase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


3-isopropylmalate dehydrogenase / 3-isopropylmalate dehydrogenase activity / L-leucine biosynthetic process / NAD binding / magnesium ion binding / cytoplasm
Similarity search - Function
Isopropylmalate/isohomocitrate dehydrogenase / Isopropylmalate Dehydrogenase / Isopropylmalate Dehydrogenase / Isocitrate/isopropylmalate dehydrogenase, conserved site / Isocitrate and isopropylmalate dehydrogenases signature. / Isopropylmalate dehydrogenase-like domain / Isocitrate/isopropylmalate dehydrogenase / Isocitrate/isopropylmalate dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-isopropylmalate dehydrogenase
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHirose, R. / Sakurai, M. / Suzuki, T. / Moriyama, H. / Sato, T. / Yamagishi, A. / Oshima, T. / Tanaka, N.
CitationJournal: To be Published
Title: Crystal Structure of IPMDH from Sulfolobus tokodaii
Authors: Hirose, R. / Sakurai, M. / Suzuki, T. / Moriyama, H. / Sato, T. / Yamagishi, A. / Oshima, T. / Tanaka, N.
History
DepositionSep 14, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8054
Polymers73,7572
Non-polymers492
Water1,49583
1
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6118
Polymers147,5134
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9620 Å2
ΔGint-102 kcal/mol
Surface area50470 Å2
MethodPISA, PQS
2
A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules

A: 3-isopropylmalate dehydrogenase
B: 3-isopropylmalate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6118
Polymers147,5134
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)67.910, 91.500, 132.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: x,-y,-z

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Components

#1: Protein 3-isopropylmalate dehydrogenase / / Beta-IPM dehydrogenase / IMDH / 3-IPM-DH


Mass: 36878.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: pET17b / Production host: Escherichia coli (E. coli)
References: UniProt: P50455, 3-isopropylmalate dehydrogenase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.73 Å3/Da / Density % sol: 55.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, MPD, magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 12, 2000
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→44.28 Å / Num. all: 20835 / Num. obs: 20835 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.8 Å2
Reflection shellResolution: 2.8→2.95 Å / % possible all: 97.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.73 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1791096.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2107 10.2 %RANDOM
Rwork0.19 ---
obs0.19 20726 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.3759 Å2 / ksol: 0.298852 e/Å3
Displacement parametersBiso mean: 39.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.14 Å20 Å20 Å2
2--1.98 Å20 Å2
3----7.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5180 0 2 83 5265
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it1.121.5
X-RAY DIFFRACTIONc_mcangle_it1.972
X-RAY DIFFRACTIONc_scbond_it2.152
X-RAY DIFFRACTIONc_scangle_it3.282.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 344 10.3 %
Rwork0.224 2980 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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