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- PDB-7cg2: Vigna radiata Epoxide hydrolase mutant -

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Basic information

Entry
Database: PDB / ID: 7cg2
TitleVigna radiata Epoxide hydrolase mutant
ComponentsEpoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolase
Function / homologyepoxide hydrolase activity / Epoxide hydrolase-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / Epoxide hydrolase
Function and homology information
Biological speciesVigna radiata (mung bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 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)37,4891
Polymers37,4891
Non-polymers00
Water4,756264
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 area12730 Å2
Unit cell
Length a, b, c (Å)70.478, 70.478, 129.487
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: 37488.543 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.: 264 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.15 M Tris-HCl, pH 8.5, 35% PEG33500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22723 / % possible obs: 99.6 % / Redundancy: 22.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.012 / Rrim(I) all: 0.054 / Rsym value: 0.052 / Χ2: 0.883 / Net I/σ(I): 65.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 26.2 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 8.694 / Num. unique obs: 1104 / CC1/2: 0.994 / Rpim(I) all: 0.086 / Rrim(I) all: 0.441 / Χ2: 0.466 / % 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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y6Y

5y6y


Resolution: 2.001→32.627 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2671 1130 5.1 %
Rwork0.2195 21025 -
obs0.2219 22155 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.89 Å2 / Biso mean: 24.97 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 2.001→32.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2557 0 0 264 2821
Biso mean---29.59 -
Num. residues----318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082633
X-RAY DIFFRACTIONf_angle_d1.0713583
X-RAY DIFFRACTIONf_chiral_restr0.076378
X-RAY DIFFRACTIONf_plane_restr0.005463
X-RAY DIFFRACTIONf_dihedral_angle_d13.832953
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.001-2.09180.39091170.3447226786
2.0918-2.20210.30191490.28312646100
2.2021-2.340.38731370.3119249494
2.34-2.52060.32211520.25592647100
2.5206-2.77410.32931560.24172646100
2.7741-3.17530.26561400.22332693100
3.1753-3.99930.22241440.1839272299
3.9993-32.53080.19581350.17082910100

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