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- PDB-8xiz: Crystal structure of an epoxide hydrolase mutant A250IC/L344V fro... -

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Basic information

Entry
Database: PDB / ID: 8xiz
TitleCrystal structure of an epoxide hydrolase mutant A250IC/L344V from Aspergillus usamii E001 at 2.17 Angstroms resolution
ComponentsMicrosomal epoxide hyddrolase
KeywordsHYDROLASE / Alpha and beta proteins / alpha/beta-Hydrolases / Styrene Oxide / Epoxide Hydrolase
Function / homologymicrosomal epoxide hydrolase / cis-stilbene-oxide hydrolase activity / Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / epoxide metabolic process / Epoxide hydrolase-like / Alpha/Beta hydrolase fold / Microsomal epoxide hyddrolase
Function and homology information
Biological speciesAspergillus usamii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.175 Å
AuthorsHu, B.C. / Lu, Z.Y. / Tang, C.D. / Hu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22308034 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Rational mutagenesis of an epoxide hydrolase and its structural mechanism for the enantioselectivity improvement toward chiral ortho-fluorostyrene oxide.
Authors: Lu, Z.Y. / Liao, X. / Jing, W.W. / Liu, K.K. / Ren, Q.G. / He, Y.C. / Hu, D.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1May 21, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microsomal epoxide hyddrolase
B: Microsomal epoxide hyddrolase


Theoretical massNumber of molelcules
Total (without water)97,0492
Polymers97,0492
Non-polymers00
Water8,377465
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.049, 51.287, 133.812
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microsomal epoxide hyddrolase


Mass: 48524.711 Da / Num. of mol.: 2 / Mutation: A250I,L344V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus usamii (mold) / Gene: EH2 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: T2B4K5, microsomal epoxide hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 465 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density meas: 0.008 Mg/m3 / Density % sol: 39.02 % / Description: Tetragonal crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate tribasic dihydrate,pH5.5,18%(w/v) polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.17→47.89 Å / Num. obs: 40335 / % possible obs: 97.83 % / Redundancy: 6.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.55
Reflection shellResolution: 2.17→2.18 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Num. unique obs: 6481 / CC1/2: 0.976 / % possible all: 97.83

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACT4data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.175→44.602 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 2148 5.33 %RANDOM
Rwork0.1623 ---
obs0.1654 40335 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.175→44.602 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 0 465 6700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076502
X-RAY DIFFRACTIONf_angle_d0.8148886
X-RAY DIFFRACTIONf_dihedral_angle_d6.5583792
X-RAY DIFFRACTIONf_chiral_restr0.051948
X-RAY DIFFRACTIONf_plane_restr0.0061146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1751-2.22570.26091640.17452294X-RAY DIFFRACTION90
2.2257-2.28140.2441470.17332501X-RAY DIFFRACTION98
2.2814-2.3430.24711700.17372517X-RAY DIFFRACTION98
2.343-2.4120.23721450.17712517X-RAY DIFFRACTION98
2.412-2.48980.26311560.17332514X-RAY DIFFRACTION98
2.4898-2.57880.27271140.18012561X-RAY DIFFRACTION98
2.5788-2.6820.26541460.17562544X-RAY DIFFRACTION99
2.682-2.80410.23861540.17292520X-RAY DIFFRACTION99
2.8041-2.95190.23711390.17452581X-RAY DIFFRACTION99
2.9519-3.13680.25121330.18142561X-RAY DIFFRACTION99
3.1368-3.37890.20251190.17522615X-RAY DIFFRACTION99
3.3789-3.71880.21611280.15652580X-RAY DIFFRACTION99
3.7188-4.25650.21281340.14262626X-RAY DIFFRACTION99
4.2565-5.36140.18271460.1362601X-RAY DIFFRACTION99
5.3614-44.6010.18281530.15842655X-RAY DIFFRACTION98

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