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- PDB-7cg6: Vigna radiata Epoxide hydrolase mutant M263Q -

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Basic information

Entry
Database: PDB / ID: 7cg6
TitleVigna radiata Epoxide hydrolase mutant M263Q
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase
Function / homologysoluble epoxide hydrolase / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / soluble epoxide hydrolase
Function and homology information
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, F.L. / Yu, H.L. / Xu, J.H.
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Reprogramming Epoxide Hydrolase to Improve Enantioconvergence in Hydrolysis of Styrene Oxide Scaffolds
Authors: Li, F.L. / Qiu, Y.Y. / Zheng, Y.C. / Chen, F.F. / Kong, X.D. / Xu, J.H. / Yu, H.L.
History
DepositionJun 30, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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


Theoretical massNumber of molelcules
Total (without water)37,5181
Polymers37,5181
Non-polymers00
Water4,630257
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 area12510 Å2
Unit cell
Length a, b, c (Å)70.813, 70.813, 127.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Epoxide hydrolase


Mass: 37517.543 Da / Num. of mol.: 1 / Mutation: M263V
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.: 257 / 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: 2.13 Å3/Da / Density % sol: 42.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.15 M Tris-HCl, pH 8.5, 35% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22019 / % possible obs: 97.1 % / Redundancy: 22 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.015 / Rrim(I) all: 0.068 / Net I/σ(I): 46.66
Reflection shellResolution: 2→2.03 Å / Redundancy: 25.3 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 4.32 / Num. unique obs: 1091 / CC1/2: 0.963 / Rsym value: 0.856 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y6Y

5y6y


Resolution: 2→34.113 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 32.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 1093 5.12 %
Rwork0.2193 20260 -
obs0.223 21353 94.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.83 Å2 / Biso mean: 26.46 Å2 / Biso min: 9.95 Å2
Refinement stepCycle: final / Resolution: 2→34.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 0 257 2816
Biso mean---29.35 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072635
X-RAY DIFFRACTIONf_angle_d1.0663585
X-RAY DIFFRACTIONf_chiral_restr0.073377
X-RAY DIFFRACTIONf_plane_restr0.006464
X-RAY DIFFRACTIONf_dihedral_angle_d13.756955
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.09080.47521230.4212222885
2.0908-2.2010.34341360.29012631100
2.201-2.33890.45721040.3294195374
2.3389-2.51950.31911470.26132642100
2.5195-2.77290.34911620.258261199
2.7729-3.17390.28091640.22422670100
3.1739-3.99780.28471260.184262796
3.9978-34.110.21861310.16542898100

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