5XO8

Crystal structure of a novel ZEN lactonase mutant with ligand Z

• PDB DOI: https://doi.org/10.2210/pdb5XO8/pdb

• Classification: HYDROLASE
• Organism(s): Rhinocladiella mackenziei CBS 650.93
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-05-27 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: 1.88 Å
• R-Value Free: 0.181 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 

Starting Model: experimental

Literature

Crystal Structure of a Mycoestrogen-Detoxifying Lactonase from Rhinocladiella mackenziei: Molecular Insight into ZHD Substrate Selectivity

Zheng, Y.Y., Liu, W.T., Chen, C.C., Hu, X.Y., Liu, W.D., Ko, T.P., Tang, X.K., Wei, H.L., Huang, J.W., Guo, R.T.

(2018) ACS Catal 8: 4294-4298

• DOI: https://doi.org/10.1021/acscatal.8b00464

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: 238.14 kDa 
• Atom Count: 19,224 
• Modelled Residue Count: 2,104 
• Deposited Residue Count: 2,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactonase for protein	A, B, C, D, E, F, G, H	266	Rhinocladiella mackenziei CBS 650.93	Mutation(s): 1  Gene Names: Z518_04590
UniProt
Find proteins for A0A0D2ILK1 (Rhinocladiella mackenziei CBS 650.93) Explore A0A0D2ILK1  Go to UniProtKB:  A0A0D2ILK1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZER	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	(3S,11E)-14,16-dihydroxy-3-methyl-3,4,5,6,9,10-hexahydro-1H-2-benzoxacyclotetradecine-1,7(8H)-dione C18 H22 O5 MBMQEIFVQACCCH-QBODLPLBSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.181 
• R-Value Work: 0.145 
• R-Value Observed: 0.146 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.47	α = 90.21
b = 95.196	β = 92.34
c = 101.663	γ = 91.48

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data scaling
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, Refinement description