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- PDB-6ix2: Structure of the A214C/A250I mutant of an epoxide hydrolase from ... -

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Basic information

Entry
Database: PDB / ID: 6ix2
TitleStructure of the A214C/A250I mutant of an epoxide hydrolase from Aspergillus usamii E001 (AuEH2) at 1.48 Angstroms resolution
ComponentsMicrosomal epoxide hyddrolase
KeywordsHYDROLASE / Alpha and beta proteins / alpha/beta-Hydrolases / Styrene Oxide
Function / homology
Function and homology information


microsomal epoxide hydrolase / cis-stilbene-oxide hydrolase activity / epoxide metabolic process / epoxide hydrolase activity
Similarity search - Function
Epoxide hydrolase, N-terminal / Epoxide hydrolase N terminus / Epoxide hydrolase / Epoxide hydrolase-like / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Microsomal epoxide hyddrolase
Similarity search - Component
Biological speciesAspergillus usamii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.478 Å
AuthorsHu, D. / Hu, B.C. / Hou, X.D. / Rao, Y.J. / Wu, M.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21676117 China
CitationJournal: Org.Lett. / Year: 2022
Title: Structure-Guided Regulation in the Enantioselectivity of an Epoxide Hydrolase to Produce Enantiomeric Monosubstituted Epoxides and Vicinal Diols via Kinetic Resolution.
Authors: Hu, D. / Hu, B.C. / Hou, X.D. / Zhang, D. / Lei, Y.Q. / Rao, Y.J. / Wu, M.C.
History
DepositionDec 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,2343
Polymers97,1422
Non-polymers921
Water18,7541041
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, Dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-31 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.365, 51.922, 133.488
Angle α, β, γ (deg.)90.000, 90.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Microsomal epoxide hyddrolase


Mass: 48570.805 Da / Num. of mol.: 2 / Mutation: A214C, A250I
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1041 / 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: 2.22 Å3/Da / Density meas: 0.008 Mg/m3 / Density % sol: 39.89 % / Description: Tetragonal crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Sodium citrate tribasic dihydrate, pH 5.5, 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 S 6M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 131152 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.41 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Χ2: 0.954 / Net I/σ(I): 9.7 / Num. measured all: 874695
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.48-1.516.70.20664810.9760.0860.2240.93599.8
1.51-1.536.60.1965170.9780.0790.2060.93799.8
1.53-1.566.40.1765140.9810.0720.1850.97499.8
1.56-1.5960.15564860.9820.0680.171.01198.9
1.59-1.636.90.14265500.9870.0580.1541.008100
1.63-1.676.90.1364970.9880.0530.140.9899.8
1.67-1.716.80.11965150.9910.0490.1290.96299.9
1.71-1.756.70.10765340.9910.0440.1160.96499.9
1.75-1.816.60.09665560.9920.040.1040.96899.9
1.81-1.866.30.08365310.9930.0360.0910.97199.7
1.86-1.936.50.07365740.9960.0310.0790.97699.8
1.93-2.016.90.06765170.9960.0270.0730.963100
2.01-2.16.90.06165760.9960.0250.0660.979100
2.1-2.216.80.05565840.9970.0230.060.966100
2.21-2.356.50.0565390.9970.0210.0550.94799.7
2.35-2.536.60.04865210.9970.020.0520.92399.2
2.53-2.797.10.04566030.9980.0180.0490.887100
2.79-3.196.90.04166390.9980.0170.0440.88799.8
3.19-4.026.50.03766220.9980.0150.040.94399.8
4.02-506.60.03767960.9980.0150.040.9299.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qo7

1qo7


Resolution: 1.478→43.867 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1783 6591 5.03 %
Rwork0.1593 124517 -
obs0.1603 131108 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 65.78 Å2 / Biso mean: 16.6843 Å2 / Biso min: 6.3 Å2
Refinement stepCycle: final / Resolution: 1.478→43.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6146 0 6 1041 7193
Biso mean--21.68 27.53 -
Num. residues----765
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4782-1.4950.18742100.16553916412695
1.495-1.51260.18641840.160841604344100
1.5126-1.5310.1832220.163741054327100
1.531-1.55040.17692010.16142044405100
1.5504-1.57080.19312100.15784099430999
1.5708-1.59230.181980.16014120431899
1.5923-1.61510.19652330.158441364369100
1.6151-1.63920.192270.156841284355100
1.6392-1.66480.18622490.163340734322100
1.6648-1.69210.20022240.167841524376100
1.6921-1.72130.1852300.166741614391100
1.7213-1.75260.18531980.164441104308100
1.7526-1.78630.20052710.164941334404100
1.7863-1.82270.1812250.159241104335100
1.8227-1.86240.17222280.160641564384100
1.8624-1.90570.1791950.151741534348100
1.9057-1.95340.18282300.156441234353100
1.9534-2.00620.17452030.157941804383100
2.0062-2.06520.19022080.160541834391100
2.0652-2.13190.19442140.158641684382100
2.1319-2.20810.1612560.155841604416100
2.2081-2.29650.16492060.155741454351100
2.2965-2.4010.17421980.16014134433299
2.401-2.52750.1772180.164741724390100
2.5275-2.68590.1922250.169242114436100
2.6859-2.89320.18052270.161641844411100
2.8932-3.18430.17092350.161541734408100
3.1843-3.64490.16752380.15141694407100
3.6449-4.59140.1732340.144642264460100
4.5914-43.88590.17421940.171243734567100

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