5ZMY

Crystal structure of a cis-epoxysuccinate hydrolase producing D(-)-tartaric acids

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history. 


Literature

Structural insight into the catalytic mechanism of a cis-epoxysuccinate hydrolase producing enantiomerically pure d(-)-tartaric acid.

Dong, S., Liu, X., Cui, G.Z., Cui, Q., Wang, X., Feng, Y.

(2018) Chem Commun (Camb) 54: 8482-8485

  • DOI: https://doi.org/10.1039/c8cc04398a
  • Primary Citation of Related Structures:  
    5ZMU, 5ZMY

  • PubMed Abstract: 

    Crystal structure determination and mutagenesis analysis of a cis-epoxysuccinate hydrolase which produces enantiomerically pure d(-)-tartaric acids revealed a zinc ion and essential residues in the stereoselective mechanism for the catalytic reaction of the small mirror symmetric substrate.

    • Organizational Affiliation: 

    Shandong Provincial Key Laboratory of Synthetic Biology and CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao, Shandong 266101, China. [email protected] [email protected].


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cis-epoxysuccinate hydrolase
A, B, C, D, E
A, B, C, D, E, F, G, H
314Bordetella sp. BK-52Mutation(s): 1 
UniProt
Find proteins for F1LJ99 (Bordetella sp. BK-52)
Explore F1LJ99 
Go to UniProtKB:  F1LJ99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1LJ99
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR
Download Ideal Coordinates CCD File 
J [auth A]
L [auth B]
N [auth C]
P [auth D]
R [auth E]
J [auth A],
L [auth B],
N [auth C],
P [auth D],
R [auth E],
T [auth F],
V [auth G],
X [auth H]
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F],
U [auth G],
W [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.159α = 90
b = 158.348β = 90
c = 134.09γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31670735

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description