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- PDB-1ek2: CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1ek2
TitleCRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED WITH CDU INHIBITOR
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / HOMODIMER / ALPHA/BETA HYDROLASE FOLD / DISUBSTITUTED UREA INHIBITOR
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
N-CYCLOHEXYL-N'-DECYLUREA / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsArgiriadi, M.A. / Morisseau, C. / Goodrow, M.H. / Dowdy, D.L. / Hammock, B.D. / Christianson, D.W.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Binding of alkylurea inhibitors to epoxide hydrolase implicates active site tyrosines in substrate activation.
Authors: Argiriadi, M.A. / Morisseau, C. / Goodrow, M.H. / Dowdy, D.L. / Hammock, B.D. / Christianson, D.W.
#1: 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.
History
DepositionMar 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPOXIDE HYDROLASE
B: EPOXIDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,7294
Polymers125,1642
Non-polymers5652
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-16 kcal/mol
Surface area39320 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
DetailsA domain-swapped homodimer constructed by chain A and B generated by two-fold symmetry. Inhibitor CDU bound in both molecules

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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) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P34914, epoxide hydrolase
#2: Chemical ChemComp-CDU / N-CYCLOHEXYL-N'-DECYLUREA


Mass: 282.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H34N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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, CDU (N-cyclohexyl-N'-decylurea), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: Argiriadi, M.A., (1999) Proc.Nat.Acad.Sci.USA, 96, 10637.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
116 mg/mlprotein1drop
23 mMdithiothreitol1drop
3100 mMsodium phosphate1drop
41.6 Mammonium sulfate1dropprecipitant
5100 mMMES1dropprecipitant
61.4 %(v/v)ethanol1drop
71.6 Mammonium sulfate1reservoir
8100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.89
DetectorType: OTHER / Detector: CCD / Date: Aug 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 51503 / Num. obs: 46217 / % possible obs: 79.4 % / Observed criterion σ(F): 2 / Redundancy: 2.34 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.5
Reflection shellResolution: 3→20 Å / Redundancy: 2.26 % / Rmerge(I) obs: 0.282 / Num. unique all: 1428 / % possible all: 58.5
Reflection
*PLUS
Num. obs: 19689 / Num. measured all: 46217
Reflection shell
*PLUS
% possible obs: 58.5 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 3→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.29 924 RANDOM
Rwork0.211 --
all-19689 -
obs-18983 -
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8178 0 40 19 8237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.6

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