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- PDB-6i5e: X-ray structure of apo human soluble Epoxide Hydrolase C-terminal... -

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Basic information

Entry
Database: PDB / ID: 6i5e
TitleX-ray structure of apo human soluble Epoxide Hydrolase C-terminal Domain (hsEH CTD)
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / hsEH CTD / apoprotein / alpha_beta hydrolase fold
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
Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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


Theoretical massNumber of molelcules
Total (without water)79,0912
Polymers79,0912
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The apoprotein crystallised as two hsEH CTD molecules in the asymmetric unit forming a homodimer. However, gel filtration analysis showed isolated monodispersed and ...Evidence: gel filtration, The apoprotein crystallised as two hsEH CTD molecules in the asymmetric unit forming a homodimer. However, gel filtration analysis showed isolated monodispersed and monomeric protein in solution.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-1 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.224, 80.139, 104.696
Angle α, β, γ (deg.)90.00, 95.39, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
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: I04 / 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: 2.6→70.51 Å / Num. all: 114202 / Num. obs: 22492 / % possible obs: 99.9 % / Redundancy: 5.077 % / Rmerge(I) obs: 0.21 / Rrim(I) all: 0.235 / Net I/σ(I): 5.7
Reflection shellResolution: 2.60012→29.6003 Å / Rmerge(I) obs: 0.741 / Rrim(I) all: 0.831

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANS

3ans


Resolution: 2.6→70.51 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.886 / SU B: 20.645 / SU ML: 0.393 / Cross valid method: THROUGHOUT / ESU R: 1.475 / ESU R Free: 0.358 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27704 1101 4.9 %RANDOM
Rwork0.24599 ---
obs0.24755 21388 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 45.454 Å2
Baniso -1Baniso -2Baniso -3
1--4.08 Å2-0 Å21.11 Å2
2---3.2 Å2-0 Å2
3---6.95 Å2
Refinement stepCycle: 1 / Resolution: 2.6→70.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 0 13 5099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195238
X-RAY DIFFRACTIONr_bond_other_d0.0020.024864
X-RAY DIFFRACTIONr_angle_refined_deg1.4491.9477104
X-RAY DIFFRACTIONr_angle_other_deg1.001311232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73223.934244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29115880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7641528
X-RAY DIFFRACTIONr_chiral_restr0.0790.2736
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215886
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021234
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_it2.7844.3912526
X-RAY DIFFRACTIONr_mcbond_other2.7784.3912525
X-RAY DIFFRACTIONr_mcangle_it4.6186.5853154
X-RAY DIFFRACTIONr_mcangle_other4.6186.5863155
X-RAY DIFFRACTIONr_scbond_it2.7894.6782712
X-RAY DIFFRACTIONr_scbond_other2.7854.6762710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7086.8993950
X-RAY DIFFRACTIONr_long_range_B_refined8.98940.94422200
X-RAY DIFFRACTIONr_long_range_B_other8.98940.94522199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 95 -
Rwork0.389 1581 -
obs--100 %

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