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- PDB-1cr6: CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED W... -

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Basic information

Entry
Database: PDB / ID: 1cr6
TitleCRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED WITH CPU INHIBITOR
ComponentsEPOXIDE HYDROLASE
KeywordsHYDROLASE / HOMODIMER / ALPHA/BETA HYDROLASE FOLD / DISUBSTITUTED UREA INHIBITOR
Function / homology
Function and homology information


prostaglandin production involved in inflammatory response / 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 / soluble epoxide hydrolase / epoxide metabolic process ...prostaglandin production involved in inflammatory response / 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 / soluble epoxide hydrolase / epoxide metabolic process / Peroxisomal protein import / lysophosphatidic acid phosphatase activity / linoleic acid metabolic process / positive regulation of blood pressure / epoxide hydrolase activity / regulation of cholesterol metabolic process / dephosphorylation / phosphatase activity / 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'-(PROPYL)PHENYL UREA / 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: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Potent urea and carbamate inhibitors of soluble epoxide hydrolases
Authors: Morisseau, C. / Goodrow, M. / Dowdy, D. / Zheng, J. / Greene, J. / Sanborn, J.R. / Hammock, B.D.
History
DepositionAug 13, 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 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)125,6854
Polymers125,1642
Non-polymers5212
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-8 kcal/mol
Surface area39070 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
Detailshomodimer, each monomer represented by chain A and chain B related by an NCS two-fold. / domain-swapped dimer

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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: Chemical ChemComp-CPU / N-CYCLOHEXYL-N'-(PROPYL)PHENYL UREA


Mass: 260.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H24N2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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 / pH: 6
Details: ammonium sulfate, MES, ethanol, dithiothreitol, CPU (N-cyclohexyl-N'-(3-phenyl)propyl urea), pH 6.0, VAPOR DIFFUSION, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
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: 0.893
DetectorType: OTHER / Detector: CCD / Date: Aug 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.893 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 73807 / Num. obs: 24877 / % possible obs: 0.916 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.9
Reflection shellResolution: 2.8→20 Å / Redundancy: 1 % / Rmerge(I) obs: 0.345 / Num. unique all: 1300 / % possible all: 0.428
Reflection
*PLUS
% possible obs: 80.1 % / Num. measured all: 73807
Reflection shell
*PLUS
% possible obs: 42.8 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.8→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1153 -RANDOM 5%
Rwork0.201 ---
all0.261 24877 --
obs0.252 22648 91 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8178 0 38 21 8237
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.013
X-RAY DIFFRACTIONx_angle_deg1.76
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_improper_angle_d0.9
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.9

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