5Y5D | pdb_00005y5d

The crystal structure of VrEH2 mutant M263W

• PDB DOI: https://doi.org/10.2210/pdb5Y5D/pdb

• Classification: HYDROLASE
• Organism(s): Vigna radiata
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-08-08 Released: 2018-12-05 
• Deposition Author(s): Xu, J.H., Yu, H.L., Zhou, J.H., Kong, X.D., Li, F.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of VrEH2 mutant M263W

Xu, J.H., Yu, H.L., Zhou, J.H., Kong, X.D., Li, F.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.39 kDa 
• Atom Count: 2,886 
• Modeled Residue Count: 318 
• Deposited Residue Count: 326 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase	A [auth B]	326	Vigna radiata	Mutation(s): 3  Gene Names: EH2 EC: 3.3.2.10
UniProt
Find proteins for A0A0R5NGA4 (Vigna radiata) Explore A0A0R5NGA4  Go to UniProtKB:  A0A0R5NGA4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.236 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.475	α = 90
b = 70.475	β = 90
c = 129.021	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-05 
Deposition Author(s): Xu, J.H., Yu, H.L., Zhou, J.H., Kong, X.D., Li, F.L.

Revision History  

• Version 1.0: 2018-12-05
  Type: Initial release
  
• Version 1.1: 2019-08-28
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description