5ZMY

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

• PDB DOI: https://doi.org/10.2210/pdb5ZMY/pdb

• Classification: HYDROLASE
• Organism(s): Bordetella sp. BK-52
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-04-06 Released: 2018-08-08 
• Deposition Author(s): Dong, S., Liu, X., Wang, X., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China

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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

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

• PubMed: 30003205 
• 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.

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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. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 278.91 kDa 
• Atom Count: 20,366 
• Modelled Residue Count: 2,233 
• Deposited Residue Count: 2,512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cis-epoxysuccinate hydrolase	A, B, C, D, E, F, G, H	314	Bordetella sp. BK-52	Mutation(s): 1
UniProt
Find proteins for F1LJ99 (Bordetella sp. BK-52) Explore F1LJ99  Go to UniProtKB:  F1LJ99

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TAR	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	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 = 135.159	α = 90
b = 158.348	β = 90
c = 134.09	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Dong, S., Liu, X., Wang, X., Feng, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31670735

Revision History  

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