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- PDB-1cqz: CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE. -

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Basic information

Entry
Database: PDB / ID: 1cqz
TitleCRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE.
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / HOMODIMER / ALPHA/BETA HYDROLASE FOLD / DOMAIN-SWAPPING
Function / homology
Function and homology information


Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Biosynthesis of maresins / lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Peroxisomal protein import / epoxide metabolic process / lysophosphatidic acid phosphatase activity ...Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / Biosynthesis of maresins / lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Peroxisomal protein import / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / epoxide hydrolase activity / dephosphorylation / regulation of cholesterol metabolic process / toxic substance binding / cholesterol homeostasis / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / cytosol
Similarity search - Function
Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / HAD superfamily/HAD-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily ...Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / HAD superfamily/HAD-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / DNA polymerase; domain 1 / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsArgiriadi, M.A. / Morisseau, C. / Hammock, B.D. / Christianson, D.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Detoxification of environmental mutagens and carcinogens: structure, mechanism, and evolution of liver epoxide hydrolase.
Authors: Argiriadi, M.A. / Morisseau, C. / Hammock, B.D. / Christianson, D.W.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Molecular cloning and expression of murine liver soluble epoxide hydrolase
Authors: Grant, D.F. / Storms, D.H. / Hammock, B.D.
#2: Journal: DNA Cell Biol. / Year: 1995
Title: Gene evolution of epoxide hydrolases and recommended nomenclature
Authors: Beetham, J.K. / Grant, D. / Arand, M. / Garbarino, J. / Kiyosue, T. / Pinot, F. / Oesch, F. / Belknap, W.R. / Shinozaki, K. / Hammock, B.D.
History
DepositionAug 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPOXIDE HYDROLASE
B: EPOXIDE HYDROLASE


Theoretical massNumber of molelcules
Total (without water)125,1642
Polymers125,1642
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-11 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.900, 143.000, 60.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein EPOXIDE HYDROLASE


Mass: 62582.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: LIVER / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34914, epoxide hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, MES, ethanol, dithiothreitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
21.5 mMdithiothreitol1drop
350 mMsodium phosphate1drop
40.72 Mammonium sulfate1drop
545 mMMES1drop
60.07 %(v/v)ethanol1drop
71.6 Mammonium sulfate1reservoir
8100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: OTHER / Detector: CCD / Date: Jul 29, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 30555 / Num. obs: 32278 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.4 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 2.8→50 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.357 / Num. unique all: 3081 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 304577 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 96.7 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.309 1598 -RANDOM 5%
Rwork0.214 ---
all0.275 32278 --
obs0.269 32278 94.6 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8178 0 0 40 8218
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d27.7
X-RAY DIFFRACTIONx_improper_angle_d1
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1

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