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- PDB-5xm6: the overall structure of VrEH2 -

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Basic information

Entry
Database: PDB / ID: 5xm6
Titlethe overall structure of VrEH2
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase
Function / homology
Function and homology information


Hydrolases; Acting on ether bonds; Ether hydrolases / 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
Epoxide hydrolase / Epoxide hydrolase
Similarity search - Component
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsLi, F.L. / Kong, X.D. / Yu, H.L. / Shang, Y.P. / 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
DepositionMay 12, 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

Downloads & links

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Assembly

Deposited unit
A: Epoxide hydrolase
B: Epoxide hydrolase
C: Epoxide hydrolase


Theoretical massNumber of molelcules
Total (without water)119,4453
Polymers119,4453
Non-polymers00
Water10,305572
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-2 kcal/mol
Surface area35970 Å2
Unit cell
Length a, b, c (Å)109.180, 109.180, 236.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Epoxide hydrolase /


Mass: 39815.141 Da / Num. of mol.: 3 / Mutation: G3E, V4I, R114H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vigna radiata (mung bean) / Gene: Vreh3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0G3F3K2, UniProt: A0A0R5NGA4*PLUS, Hydrolases; Acting on ether bonds; Ether hydrolases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 3.25 Å3/Da / Density % sol: 62.1 % / Description: rhombus
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 20000, PEG500MME, HEPES, Mops, sodium nitrate, ammonium sulfate, disodium hydrogen phosphate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 50435 / % possible obs: 100 % / Redundancy: 27.9 % / CC1/2: 0.987 / Rpim(I) all: 0.031 / Χ2: 1.022 / Net I/σ(I): 8.25
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 29.5 % / Num. unique obs: 4938 / CC1/2: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4i6.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CJP

2cjp


Resolution: 2.501→41.532 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.78
RfactorNum. reflection% reflection
Rfree0.2231 2556 5.08 %
Rwork0.18 --
obs0.1822 50310 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.501→41.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7678 0 0 572 8250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087906
X-RAY DIFFRACTIONf_angle_d1.11910757
X-RAY DIFFRACTIONf_dihedral_angle_d14.1362868
X-RAY DIFFRACTIONf_chiral_restr0.0771132
X-RAY DIFFRACTIONf_plane_restr0.0061392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.54910.28931340.20962586X-RAY DIFFRACTION99
2.5491-2.60110.28111500.20562614X-RAY DIFFRACTION100
2.6011-2.65770.29481280.21292611X-RAY DIFFRACTION100
2.6577-2.71950.26181370.19672620X-RAY DIFFRACTION100
2.7195-2.78750.2531350.19682600X-RAY DIFFRACTION100
2.7875-2.86280.24461510.19142610X-RAY DIFFRACTION100
2.8628-2.9470.26031430.19832624X-RAY DIFFRACTION100
2.947-3.04210.24131380.19642619X-RAY DIFFRACTION100
3.0421-3.15080.25291380.19122625X-RAY DIFFRACTION100
3.1508-3.27690.28621280.19762629X-RAY DIFFRACTION100
3.2769-3.4260.22481430.18182658X-RAY DIFFRACTION100
3.426-3.60650.19031420.17942628X-RAY DIFFRACTION100
3.6065-3.83230.21541410.17562659X-RAY DIFFRACTION100
3.8323-4.1280.19711560.16072649X-RAY DIFFRACTION100
4.128-4.54290.17851610.14942695X-RAY DIFFRACTION100
4.5429-5.19920.20261360.15222698X-RAY DIFFRACTION100
5.1992-6.54630.20881510.19092731X-RAY DIFFRACTION100
6.5463-41.53820.20781440.17952898X-RAY DIFFRACTION99

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