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- PDB-6ix4: Structure of an epoxide hydrolase from Aspergillus usamii E001 (A... -

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Basic information

Entry
Database: PDB / ID: 6ix4
TitleStructure of an epoxide hydrolase from Aspergillus usamii E001 (AuEH2) at 1.51 Angstroms resolution
ComponentsMicrosomal epoxide hydrolase
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
ACETATE ION / Microsomal epoxide hyddrolase
Similarity search - Component
Biological speciesAspergillus usamii (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.511 Å
AuthorsHu, D. / Hu, B.C. / Hou, X.D. / Wu, L. / Rao, Y.J. / Wu, M.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21676117 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2021
Title: Nearly perfect kinetic resolution of racemic o-nitrostyrene oxide by AuEH2, a microsomal epoxide hydrolase from Aspergillus usamii, with high enantio- and regio-selectivity.
Authors: Hu, D. / Hu, B.C. / Wen, Z. / Zhang, D. / Liu, Y.Y. / Zang, 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 23, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _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 hydrolase
B: Microsomal epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,0777
Polymers89,7712
Non-polymers3065
Water17,294960
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, DIMERIC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-57 kcal/mol
Surface area28770 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

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Protein , 1 types, 2 molecules AB

#1: Protein Microsomal epoxide hydrolase


Mass: 44885.688 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 965 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 960 / 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: 2.05 Å3/Da / Density meas: 0.008 Mg/m3 / Density % sol: 44.45 % / Description: Tetragonal crystal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M HEPES, pH 6.5, 25%(w/v) Polyethylene glycol 3350

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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: 1.51→50 Å / Num. obs: 122867 / % possible obs: 99.6 % / Redundancy: 6.7 % / Biso Wilson estimate: 12.67 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.025 / Rrim(I) all: 0.066 / Χ2: 0.962 / Net I/σ(I): 7.9 / Num. measured all: 823528
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.51-1.546.60.27161030.9640.1130.2940.99899.3
1.54-1.566.40.24860240.9660.1050.2691.01798.9
1.56-1.596.10.22860510.970.0990.2491.03698.2
1.59-1.636.90.20961130.9790.0840.2251.04199.5
1.63-1.666.90.19160640.9830.0770.206199.7
1.66-1.76.90.17961230.9840.0730.1931.00399.7
1.7-1.746.80.15761800.9860.0640.170.99599.8
1.74-1.796.70.14161160.9880.0580.153199.7
1.79-1.846.50.12461260.990.0520.1340.9899.7
1.84-1.96.20.160230.9930.0430.1090.9998.9
1.9-1.9770.09461760.9950.0380.1011.007100
1.97-2.056.90.08161610.9950.0330.0870.993100
2.05-2.146.90.0761490.9960.0290.0760.969100
2.14-2.266.80.06261700.9970.0250.0670.97100
2.26-2.46.30.05461160.9970.0230.0580.90899.3
2.4-2.5870.05161850.9980.020.0550.911100
2.58-2.847.10.04661770.9980.0190.050.875100
2.84-3.256.80.03962290.9980.0160.0420.856100
3.25-4.16.60.03362160.9980.0140.0360.87599.5
4.1-506.70.03263650.9990.0130.0340.82499.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
AMPLEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1qo7

1qo7


Resolution: 1.511→43.867 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.37 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.1651 6064 4.94 %
Rwork0.1441 116770 -
obs0.1452 122834 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.8 Å2 / Biso mean: 16.4513 Å2 / Biso min: 6.77 Å2
Refinement stepCycle: final / Resolution: 1.511→43.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 17 960 7233
Biso mean--20.97 27.42 -
Num. residues----781
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 (%)
1.5106-1.52770.16061800.14963801398197
1.5277-1.54570.18972040.14773865406999
1.5457-1.56450.18492010.1483801400299
1.5645-1.58430.18741680.14963866403498
1.5843-1.60520.1722060.14663816402299
1.6052-1.62720.17111850.13539134098100
1.6272-1.65040.16971670.138739154082100
1.6504-1.67510.18692100.142138684078100
1.6751-1.70120.18741990.152338494048100
1.7012-1.72910.19051760.146339534129100
1.7291-1.7590.18271820.146338814063100
1.759-1.79090.16672130.143539024115100
1.7909-1.82540.18411660.147338774043100
1.8254-1.86260.16441960.14513894409099
1.8626-1.90310.17152190.13953807402699
1.9031-1.94740.17851920.13638864078100
1.9474-1.99610.16172140.140539654179100
1.9961-2.05010.16941880.144238914079100
2.0501-2.11040.14881940.142938844078100
2.1104-2.17850.17092360.141538794115100
2.1785-2.25640.1732250.144139084133100
2.2564-2.34670.1712290.144638594088100
2.3467-2.45350.17132120.14743854406699
2.4535-2.58290.19511900.150839574147100
2.5829-2.74470.16122150.148639214136100
2.7447-2.95650.15372340.14638814115100
2.9565-3.2540.14582170.146139394156100
3.254-3.72460.14532140.13643922413699
3.7246-4.69180.13552000.129939704170100
4.6918-43.8850.18722320.160640464278100

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