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- PDB-6hgw: Soluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4... -

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Basic information

Entry
Database: PDB / ID: 6hgw
TitleSoluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4-phenoxybenzyl)ethanamine
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / Inhibitor / Complex / 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 / 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-G3W / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.407 Å
AuthorsKramer, J.S. / Pogoryelov, D. / Hiesinger, K. / Proschak, E.
Funding support Germany, 1items
OrganizationGrant numberCountry
Else-Kroener-Fresenius Stiftung TRIP Graduate School Germany
CitationJournal: To Be Published
Title: Soluble epoxide hydrolase in complex with 2-(4-fluorophenyl)-N-(4-phenoxybenzyl)ethanamine
Authors: Kramer, J.S. / Pogoryelov, D. / Hiesinger, K. / Proschak, E.
History
DepositionAug 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 7, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 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 1.2Jan 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)39,9702
Polymers39,6491
Non-polymers3211
Water50428
1
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9404
Polymers79,2972
Non-polymers6432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)80.180, 92.420, 106.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 39648.531 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-G3W / 2-(4-fluorophenyl)-~{N}-[(4-phenoxyphenyl)methyl]ethanamine


Mass: 321.388 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20FNO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant ...Details: 1 uL protein solution Protein (5-10 mg/mL , 50 mM NaCl, 50 mM sodium phosphate, 10% glycerol (98%), 2 mM DTT at pH 7.4) was mixed in different ratios (2/1, 1/1, 1/2) with precipitant solution (23 %-28 % (w/v) polyethylenglycol (PEG) 6000, 70 mM ammonium acetat, 200 mM magnesium acetat, 100 mM sodium cacodylate at pH 6.1-6.5)
PH range: 6.0-6.55

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2017
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.407→53.265 Å / Num. obs: 15705 / % possible obs: 100 % / Redundancy: 12.928 % / Biso Wilson estimate: 52.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.116 / Χ2: 0.976 / Net I/σ(I): 15.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.41-2.4712.8441.3312.0811410.7571.387100
2.47-2.5412.9431.132.5111220.8541.176100
2.54-2.6112.3240.8383.2910820.9060.875100
2.61-2.6913.2820.654.5310430.9410.676100
2.69-2.7813.4060.5565.3210300.960.579100
2.78-2.8813.360.4266.749850.9810.444100
2.88-2.9913.0160.3518.149650.9840.366100
2.99-3.1112.6220.25410.79210.9890.265100
3.11-3.2512.420.18713.558900.9950.195100
3.25-3.413.6630.16116.398460.9960.167100
3.4-3.5913.5430.11421.357970.9970.118100
3.59-3.8113.3180.09924.467790.9970.103100
3.81-4.0712.6390.07927.717340.9980.082100
4.07-4.3912.7510.06731.516660.9980.07100
4.39-4.8113.3770.06335.216280.9980.065100
4.81-5.3813.0560.06435.135730.9980.067100
5.38-6.2211.9770.06831.645110.9980.071100
6.22-7.6112.8740.06435.034350.9970.066100
7.61-10.7612.0990.05140.613450.9980.053100
10.76-53.26510.3490.05138.722120.9970.05499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FR2

6fr2


Resolution: 2.407→53.265 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.98
RfactorNum. reflection% reflection
Rfree0.2388 1569 10 %
Rwork0.1804 --
obs0.1861 15694 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.27 Å2 / Biso mean: 63.0474 Å2 / Biso min: 31.41 Å2
Refinement stepCycle: final / Resolution: 2.407→53.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 24 28 2600
Biso mean--102.72 52.07 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052675
X-RAY DIFFRACTIONf_angle_d0.7413631
X-RAY DIFFRACTIONf_chiral_restr0.047375
X-RAY DIFFRACTIONf_plane_restr0.006469
X-RAY DIFFRACTIONf_dihedral_angle_d23.352988
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4071-2.48480.35871420.29112681410
2.4848-2.57360.28071380.253212431381
2.5736-2.67660.26171420.209212791421
2.6766-2.79850.33521430.213512821425
2.7985-2.9460.2551360.207612371373
2.946-3.13050.2681430.204812861429
3.1305-3.37220.25361430.189812821425
3.3722-3.71150.22591420.165912821424
3.7115-4.24840.21511430.156812871430
4.2484-5.35170.17481460.147413091455
5.3517-53.2780.26021510.184513701521
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.50962.69350.71845.4890.57314.1958-0.14680.08430.1783-0.42740.13020.1462-0.08170.0654-0.03470.312-0.02680.02350.29940.01340.3418-5.5553-6.6033-36.5311
22.66560.4063-0.49383.1143-0.29572.0529-0.0658-0.1734-0.2685-0.09160.0071-0.28350.23890.08380.07440.2922-0.00570.02350.32410.01520.373-3.3719-16.5968-31.5347
32.2582-2.0209-0.39482.1746-0.44585.6506-0.81170.0194-1.3983-0.18260.30240.37251.0722-0.40680.32550.9369-0.14150.15530.6594-0.02780.8724-13.1756-31.445-44.9697
45.59550.1862-3.10274.26114.57987.0307-0.53810.2521-0.9475-0.41960.25480.50730.7034-0.63830.25870.5928-0.099-0.11550.58970.02320.698-24.8149-23.1807-45.9599
53.2676-0.47780.08433.8781-0.39853.0797-0.043-0.1225-0.1928-0.16640.0930.06920.1443-0.1018-0.05490.358-0.06330.04390.31490.0260.3469-13.0713-20.1936-30.4202
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 229 through 270 )A229 - 270
2X-RAY DIFFRACTION2chain 'A' and (resid 271 through 370 )A271 - 370
3X-RAY DIFFRACTION3chain 'A' and (resid 371 through 399 )A371 - 399
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 435 )A400 - 435
5X-RAY DIFFRACTION5chain 'A' and (resid 436 through 547 )A436 - 547

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