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- PDB-5y6y: The crystal structure of VrEH2 mutant M263N -

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Basic information

Entry
Database: PDB / ID: 5y6y
TitleThe crystal structure of VrEH2 mutant M263N
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide Hydrolase
Function / homology
Function and homology information


soluble epoxide hydrolase / hydrolase activity
Similarity search - Function
Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
soluble epoxide hydrolase
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLi, F.L. / Yu, H.L. / Chen, Q. / Kong, X.D. / Zhou, J.H. / Xu, J.H.
CitationJournal: Acs Catalysis / Year: 2018
Title: Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation
Authors: Li, F.L. / Kong, X.D. / Chen, Q. / Zheng, Y.C. / Xu, Q. / Chen, F.F. / Fan, L.Q. / Lin, G.Q. / Zhou, J.H. / Yu, H.L. / Xu, J.H.
History
DepositionAug 15, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)37,3161
Polymers37,3161
Non-polymers00
Water6,305350
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12770 Å2
Unit cell
Length a, b, c (Å)69.769, 69.769, 130.515
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Epoxide hydrolase


Mass: 37316.250 Da / Num. of mol.: 1 / Mutation: G3E,V4I, M263N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: EH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R5NGA4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, Tri-HCL, ethylene glycol / PH range: 8.3-8.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 52501 / % possible obs: 99.6 % / Redundancy: 20.3 % / Rmerge(I) obs: 0.112 / Rsym value: 0.094 / Χ2: 1.076 / Net I/σ(I): 27.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.702 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2545 / CC1/2: 0.896 / Rpim(I) all: 0.274 / Rsym value: 1.069 / Χ2: 0.834 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XMD

5xmd


Resolution: 1.5→49.334 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 2619 5.09 %
Rwork0.1751 --
obs0.1763 51453 97.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→49.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2558 0 0 350 2908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072634
X-RAY DIFFRACTIONf_angle_d1.1033584
X-RAY DIFFRACTIONf_dihedral_angle_d12.858954
X-RAY DIFFRACTIONf_chiral_restr0.076377
X-RAY DIFFRACTIONf_plane_restr0.006464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4972-1.52440.26891220.22112006X-RAY DIFFRACTION78
1.5244-1.55370.23481180.20152305X-RAY DIFFRACTION88
1.5537-1.58540.20221380.19612414X-RAY DIFFRACTION94
1.5854-1.61990.2211410.18812562X-RAY DIFFRACTION99
1.6199-1.65760.20051390.17842558X-RAY DIFFRACTION99
1.6576-1.69910.22031540.18262579X-RAY DIFFRACTION100
1.6991-1.7450.22171450.17572566X-RAY DIFFRACTION100
1.745-1.79640.20251360.18082587X-RAY DIFFRACTION100
1.7964-1.85430.1961370.16672615X-RAY DIFFRACTION100
1.8543-1.92060.19921440.16912581X-RAY DIFFRACTION100
1.9206-1.99750.16821220.16882654X-RAY DIFFRACTION100
1.9975-2.08840.2051380.16062586X-RAY DIFFRACTION100
2.0884-2.19850.191240.16042658X-RAY DIFFRACTION100
2.1985-2.33630.1951410.16822624X-RAY DIFFRACTION100
2.3363-2.51670.17271470.17052641X-RAY DIFFRACTION100
2.5167-2.76990.19171420.17492645X-RAY DIFFRACTION100
2.7699-3.17060.20431490.18392685X-RAY DIFFRACTION100
3.1706-3.99440.17871390.16642721X-RAY DIFFRACTION100
3.9944-49.36090.20841430.18392847X-RAY DIFFRACTION99

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