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- PDB-6i5g: X-ray structure of human soluble Epoxide Hydrolase C-terminal Dom... -

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Basic information

Entry
Database: PDB / ID: 6i5g
TitleX-ray structure of human soluble Epoxide Hydrolase C-terminal Domain (hsEH CTD)in complex with 15d-PGJ2
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / hsEH CTD / apoprotein / alpha_beta hydrolase fold / 15d-PGJ2
Function / homology
Function and homology information


lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) ...lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / epoxide metabolic process / Biosynthesis of maresins / soluble epoxide hydrolase / lysophosphatidic acid phosphatase activity / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / dephosphorylation / cholesterol homeostasis / Peroxisomal protein import / response to toxic substance / peroxisome / positive regulation of gene expression / magnesium ion binding / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / haloacid dehalogenase-like hydrolase / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PTG / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAbis, G. / Kopec, J. / Yue, W.W. / Conte, M.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
British Heart FoundationPG/15/26/31373 United Kingdom
CitationJournal: Commun Biol / Year: 2019
Title: 15-deoxy-Delta12,14-Prostaglandin J2inhibits human soluble epoxide hydrolase by a dual orthosteric and allosteric mechanism.
Authors: Abis, G. / Charles, R.L. / Kopec, J. / Yue, W.W. / Atkinson, R.A. / Bui, T.T.T. / Lynham, S. / Popova, S. / Sun, Y.B. / Fraternali, F. / Eaton, P. / Conte, M.R.
History
DepositionNov 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
B: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,46816
Polymers79,0912
Non-polymers1,37814
Water4,071226
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

B: Bifunctional epoxide hydrolase 2
hetero molecules


  • defined by author
  • Evidence: gel filtration, The apoprotein crystallised with two hsEH CTD molecules in the asymmetric unit forming a homodimer. However, gel filtration experiments isolated the protein as monodispersed ...Evidence: gel filtration, The apoprotein crystallised with two hsEH CTD molecules in the asymmetric unit forming a homodimer. However, gel filtration experiments isolated the protein as monodispersed and monomeric in solution.
  • 80.5 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)80,46816
Polymers79,0912
Non-polymers1,37814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Unit cell
Length a, b, c (Å)89.490, 79.992, 104.544
Angle α, β, γ (deg.)90.00, 96.78, 90.00
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 39545.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli (E. coli)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PTG / (5E,14E)-11-oxoprosta-5,9,12,14-tetraen-1-oic acid / 15-deoxy-delta(12,14)-prostaglandin J2


Mass: 316.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H28O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.35 Å3/Da / Density % sol: 47.64 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 22.5% PEG 3350, 0.2 M malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→71.83 Å / Num. obs: 48933 / % possible obs: 99.2 % / Redundancy: 4.99 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.053 / Rrim(I) all: 0.121 / Net I/σ(I): 10.2
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.702 / Rpim(I) all: 0.354 / Rrim(I) all: 0.79

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANS

3ans


Resolution: 2→71.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.594 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.151 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21699 2403 4.9 %RANDOM
Rwork0.17203 ---
obs0.1743 46528 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å2-0 Å21.33 Å2
2---2.17 Å2-0 Å2
3---1.35 Å2
Refinement stepCycle: 1 / Resolution: 2→71.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5088 0 94 226 5408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195341
X-RAY DIFFRACTIONr_bond_other_d0.0030.025007
X-RAY DIFFRACTIONr_angle_refined_deg2.0621.9597220
X-RAY DIFFRACTIONr_angle_other_deg1.212311558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19723.934244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5811528
X-RAY DIFFRACTIONr_chiral_restr0.1470.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215962
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021254
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7693.1352534
X-RAY DIFFRACTIONr_mcbond_other2.7683.1362535
X-RAY DIFFRACTIONr_mcangle_it3.914.6873166
X-RAY DIFFRACTIONr_mcangle_other3.9094.6883167
X-RAY DIFFRACTIONr_scbond_it3.6793.5512807
X-RAY DIFFRACTIONr_scbond_other3.6783.5532808
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5465.1554050
X-RAY DIFFRACTIONr_long_range_B_refined7.34925.5856240
X-RAY DIFFRACTIONr_long_range_B_other7.34925.5946241
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 153 -
Rwork0.254 3173 -
obs--91.63 %

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