5XWZ

Crystal structure of a lactonase from Cladophialophora bantiana

• PDB DOI: https://doi.org/10.2210/pdb5XWZ/pdb

• Classification: HYDROLASE
• Organism(s): Cladophialophora bantiana CBS 173.52
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-06-30 Released: 2018-05-02 
• Deposition Author(s): Zheng, Y.Y., Liu, W.T., Liu, W.D., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.181 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

Characterization and crystal structure of a novel zearalenone hydrolase from Cladophialophora bantiana

Hui, R., Hu, X., Liu, W., Liu, W., Zheng, Y., Chen, Y., Guo, R.T., Jin, J., Chen, C.C.

(2017) Acta Crystallogr F Struct Biol Commun 73: 515-519

• PubMed: 28876230 
• DOI: https://doi.org/10.1107/S2053230X17011840
• Primary Citation of Related Structures:  
  5XWZ


• PubMed Abstract: 
  

  Zearalenone (ZEN) is a mycotoxin which causes huge economic losses in the food and animal feed industries. The lactonase ZHD101 from Clonostachys rosea, which catalyzes the hydrolytic degradation of ZEN, is the only known ZEN-detoxifying enzyme. Here, a protein homologous to ZHD101, denoted CbZHD, from Cladophialophora batiana was expressed and characterized. Sequence alignment indicates that CbZHD possesses the same catalytic triad and ZEN-interacting residues as found in ZHD101. CbZHD exhibits optimal enzyme activity at 35°C and pH 8, and is sensitive to heat treatment. The crystal structure of apo CbZHD was determined to 1.75 Å resolution. The active-site compositions of CbZHD and ZHD101 were analyzed.

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Organizational Affiliation: 

School of Pharmaceutical Sciences, Jiangnan University, 1800 Lihu Avenue, Binhu District, Wuxi, Jiangsu 214122, People's Republic of China.

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)

Macromolecule Content

• Total Structure Weight: 120.31 kDa 
• Atom Count: 9,193 
• Modelled Residue Count: 1,048 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unplaced genomic scaffold supercont1.36, whole genome shotgun sequence	A, B, C, D	271	Cladophialophora bantiana CBS 173.52	Mutation(s): 0  Gene Names: Z519_12792
UniProt
Find proteins for A0A0D2H023 (Cladophialophora bantiana CBS 173.52) Explore A0A0D2H023  Go to UniProtKB:  A0A0D2H023

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	F [auth A], M [auth D]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	G [auth B], H [auth B], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth A], I [auth B], J [auth C], L [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.181 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.863	α = 90
b = 104.399	β = 90
c = 116.834	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Zheng, Y.Y., Liu, W.T., Liu, W.D., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description