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- PDB-5yb5: The complex crystal structure of VrEH2 mutant M263N with SNO -

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Basic information

Entry
Database: PDB / ID: 5yb5
TitleThe complex crystal structure of VrEH2 mutant M263N with SNO
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase / Styrene oxide.
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
(S)-PARA-NITROSTYRENE OXIDE / soluble epoxide hydrolase
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.903 Å
AuthorsLi, F.L. / Chen, F.F. / Chen, Q. / Kong, X.D. / Yu, H.L. / 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
DepositionSep 3, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4812
Polymers37,3161
Non-polymers1651
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint6 kcal/mol
Surface area12360 Å2
Unit cell
Length a, b, c (Å)70.297, 70.297, 121.295
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: Chemical ChemComp-SNO / (S)-PARA-NITROSTYRENE OXIDE / (2S)-2-(4-NITROPHENYL)OXIRANE


Mass: 165.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.01 Å3/Da / Density % sol: 38.74 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 3350, Tris-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 S 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: 1.9→50 Å / Num. obs: 24144 / % possible obs: 98.1 % / Redundancy: 16 % / Net I/σ(I): 14.494
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 16.3 % / Mean I/σ(I) obs: 2.16 / CC1/2: 0.666 / % possible all: 97.2

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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: 1.903→45.92 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1234 5.12 %
Rwork0.1929 --
obs0.1956 24122 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.903→45.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 12 150 2721
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092648
X-RAY DIFFRACTIONf_angle_d1.1783604
X-RAY DIFFRACTIONf_dihedral_angle_d13.981955
X-RAY DIFFRACTIONf_chiral_restr0.081378
X-RAY DIFFRACTIONf_plane_restr0.006467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9033-1.97950.39971260.30292436X-RAY DIFFRACTION96
1.9795-2.06960.3221600.27282458X-RAY DIFFRACTION97
2.0696-2.17870.30781230.24352487X-RAY DIFFRACTION98
2.1787-2.31520.31041320.23542497X-RAY DIFFRACTION98
2.3152-2.4940.30441490.22292505X-RAY DIFFRACTION98
2.494-2.74490.30031320.21292532X-RAY DIFFRACTION98
2.7449-3.1420.25491540.20042556X-RAY DIFFRACTION99
3.142-3.95830.23551200.1782631X-RAY DIFFRACTION99
3.9583-45.93330.20171380.16472786X-RAY DIFFRACTION99

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