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- PDB-9jfm: Co-crystal Structure of sEH with tetrahydroberberine derivative -

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Basic information

Entry
Database: PDB / ID: 9jfm
TitleCo-crystal Structure of sEH with tetrahydroberberine derivative
ComponentsBifunctional epoxide hydrolase 2
KeywordsHYDROLASE / complex / small molecule / tetrahydroberberine derivative
Function / homology
Function and homology information


lipid-phosphate phosphatase / 10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity / stilbene catabolic process / phospholipid dephosphorylation / lipid phosphatase activity / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / 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 / Biosynthesis of maresins / epoxide metabolic process / lysophosphatidic acid phosphatase activity / soluble epoxide hydrolase / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / epoxide hydrolase activity / dephosphorylation / regulation of cholesterol metabolic process / phosphatase activity / peroxisomal matrix / toxic substance binding / Peroxisomal protein import / cholesterol homeostasis / regulation of cell growth / 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 / alpha/beta hydrolase fold / haloacid dehalogenase-like hydrolase / Alpha/beta hydrolase fold-1 / HAD superfamily / HAD-like superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / PHOSPHATE ION / Bifunctional epoxide hydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsWang, H. / Feng, Y. / Du, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Co-crystal Structure of sEH with tetrahydroberberine derivative
Authors: Wang, H. / Feng, Y. / Du, X.Y.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3324
Polymers62,6861
Non-polymers6473
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bifunctional epoxide hydrolase 2
hetero molecules

A: Bifunctional epoxide hydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,6658
Polymers125,3712
Non-polymers1,2946
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4900 Å2
ΔGint-48 kcal/mol
Surface area42830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.890, 91.890, 244.960
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein Bifunctional epoxide hydrolase 2


Mass: 62685.617 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-A1EBK / 1-[(13~{a}~{R})-2,3-dimethoxy-6,8,13,13~{a}-tetrahydro-5~{H}-isoquinolino[3,2-a]isoquinolin-10-yl]-3-[[4-(trifluoromethyloxy)phenyl]methyl]urea


Mass: 527.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H28F3N3O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.13→36.75 Å / Num. obs: 11492 / % possible obs: 99.79 % / Redundancy: 36.7 % / Biso Wilson estimate: 62.33 Å2 / CC1/2: 0.994 / Net I/σ(I): 15.93
Reflection shellResolution: 3.13→3.24 Å / Num. unique obs: 1115 / CC1/2: 0.898

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZD3

1zd3


Resolution: 3.13→36.75 Å / SU ML: 0.3152 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2658
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2262 546 4.75 %
Rwork0.192 10943 -
obs0.1936 11489 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.26 Å2
Refinement stepCycle: LAST / Resolution: 3.13→36.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4339 0 44 0 4383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00284490
X-RAY DIFFRACTIONf_angle_d0.57916088
X-RAY DIFFRACTIONf_chiral_restr0.0394662
X-RAY DIFFRACTIONf_plane_restr0.0122792
X-RAY DIFFRACTIONf_dihedral_angle_d16.9261704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.13-3.440.28731430.23352640X-RAY DIFFRACTION99.96
3.45-3.940.24181320.19952672X-RAY DIFFRACTION100
3.94-4.960.20081340.17412717X-RAY DIFFRACTION99.93
4.97-36.750.21011370.18582914X-RAY DIFFRACTION99.84

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