5XM6 | pdb_00005xm6

the overall structure of VrEH2

• PDB DOI: https://doi.org/10.2210/pdb5XM6/pdb

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


• Deposited: 2017-05-12 Released: 2018-09-05 
• Deposition Author(s): Li, F.L., Kong, X.D., Yu, H.L., Shang, Y.P., Zhou, J.H., Xu, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.223 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Regioselectivity Engineering of Epoxide Hydrolase: Near-Perfect Enantioconvergence through a Single Site Mutation

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.

(2018) ACS Catal 8: 8314-8317

• DOI: https://doi.org/10.1021/acscatal.8b02622

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 119.45 kDa 
• Atom Count: 8,249 
• Modeled Residue Count: 954 
• Deposited Residue Count: 1,056 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epoxide hydrolase	A, B, C	352	Vigna radiata	Mutation(s): 3  Gene Names: Vreh3 EC: 3.3.2 (PDB Primary Data), 3.3.2.10 (UniProt)
UniProt
Find proteins for A0A0R5NGA4 (Vigna radiata) Explore A0A0R5NGA4  Go to UniProtKB:  A0A0R5NGA4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.223 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.18	α = 90
b = 109.18	β = 90
c = 236.967	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4i	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Li, F.L., Kong, X.D., Yu, H.L., Shang, Y.P., Zhou, J.H., Xu, J.H.

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description