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- PDB-5mwa: human sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-ph... -

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Basic information

Entry
Database: PDB / ID: 5mwa
Titlehuman sEH Phosphatase in complex with 3-4-3,4-dichlorophenyl-5-phenyl-1,3-oxazol-2-yl-benzoic-acid
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Phosphatase / Complex / Inhibitor / Magnesium / human soluble epoxide hydrolase / sEH
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 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily ...Predicted HAD-superfamily phosphatase, subfamily IA/Epoxide hydrolase, N-terminal / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / Epoxide hydrolase-like / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-8S9 / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKramer, J.S. / Pogoryelov, D. / Sorrell, F.J. / Fox, N. / Chaikuad, A. / Knapp, S. / Proschak, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB1039/A07 Germany
CitationJournal: J.Med.Chem. / Year: 2019
Title: Discovery of first in vivo active inhibitors of soluble epoxide hydrolase (sEH) phosphatase domain.
Authors: Kramer, J.S. / Woltersdorf, S. / Duflot, T. / Hiesinger, K. / Lillich, F.F. / Knoll, F. / Wittmann, S.K. / Klingler, F.M. / Brunst, S. / Chaikuad, A. / Morisseau, C. / Hammock, B.D. / ...Authors: Kramer, J.S. / Woltersdorf, S. / Duflot, T. / Hiesinger, K. / Lillich, F.F. / Knoll, F. / Wittmann, S.K. / Klingler, F.M. / Brunst, S. / Chaikuad, A. / Morisseau, C. / Hammock, B.D. / Buccellati, C. / Sala, A. / Rovati, G.E. / Leuillier, M. / Fraineau, S. / Rondeaux, J. / Hernandez Olmos, V. / Heering, J. / Merk, D. / Pogoryelov, D. / Steinhilber, D. / Knapp, S. / Bellien, J. / Proschak, E.
History
DepositionJan 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 24, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Mar 31, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.4Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8353
Polymers27,4011
Non-polymers4352
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.090, 54.110, 75.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 27400.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPHX2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P34913, soluble epoxide hydrolase, lipid-phosphate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-8S9 / 3-[4-(3,4-dichlorophenyl)-5-phenyl-1,3-oxazol-2-yl]benzoic acid


Mass: 410.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H13Cl2NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.28 Å3/Da / Density % sol: 46.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein solution: 20 mM Tris, 100 mM NaCl, 0,5 mM TCEP, pH7.5 (HCl) with 30mg/mL protein and 2,08% of a 50 mM inhibitor DMSO stock Precipitant solution: 25% PEG3350 - 0,1M bis-tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Oxford Instruments Cryojet XL
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
Details: Kirkpatrick Baez (KB) bimorph mirror pair for horizontal and vertical focussing
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.55→42.86 Å / Num. obs: 31021 / % possible obs: 89 % / Observed criterion σ(F): 1.55 / Redundancy: 6.4 % / Biso Wilson estimate: 14.31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07485 / Net I/σ(I): 12.39
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.56 / CC1/2: 0.709 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
xia20.4.0.291-ga780859-dials-1.1data reduction
SCALAdata scaling
PHENIX(1.10.1_2155: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5alu
Resolution: 1.55→42.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2307 1420 5.04 %random
Rwork0.2035 ---
obs0.2049 28202 89.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.49 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 29 103 1766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_angle_d1.232279
X-RAY DIFFRACTIONf_dihedral_angle_d17.769632
X-RAY DIFFRACTIONf_chiral_restr0.478264
X-RAY DIFFRACTIONf_plane_restr0.009288
LS refinement shellResolution: 3.3391→42.86 Å
RfactorNum. reflection% reflection
Rfree0.235 163 -
Rwork0.1951 3184 -
obs--100 %

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