Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 173.65 kDa 
• Atom Count: 11777 
• Modelled Residue Count: 1348 
• Deposited Residue Count: 1530 
• Unique protein chains: 1

5Z6P

The crystal structure of an agarase, AgWH50C

• PDB DOI: 10.2210/pdb5Z6P/pdb

• Classification: HYDROLASE
• Organism(s): Agarivorans gilvus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-01-24 Released: 2019-01-02 
• Deposition Author(s): Mao, X., Zhou, J., Zhang, P., Zhang, L., Zhang, J., Li, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.245 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Structure-based design of agarase AgWH50C from Agarivorans gilvus WH0801 to enhance thermostability.

Zhang, P., Zhang, J., Zhang, L., Sun, J., Li, Y., Wu, L., Zhou, J., Xue, C., Mao, X.

(2019) Appl Microbiol Biotechnol 103: 1289-1298

• PubMed: 30523371 
• DOI: 10.1007/s00253-018-9540-1
• Primary Citation of Related Structures:  
  5Z6P


• PubMed Abstract: 
  

AgWH50C, an exo-β-agarase of GH50 isolated from Agarivorans gilvus WH0801, plays a key role in the enzymatic production of neoagarobiose, which has great application prospect in the cosmetics and pharmaceutical industry. In contrast, the poor thermostability becomes the main obstructive factor of glycoside hydrolase (GH) family 50 agarases, including AgWH50C. Herein, based on the AgWH50C crystal structure, we designed several mutants by a multiple cross-linked rational design protocol used thermostability predicting softwares ETSS, PoPMuSiC, and HotMuSiC. To our surprise, the mutant K621F increased its relative activity by as much as 45% and the optimal temperature increased to 38 °C compared to that of wild-type, AgWH50C (30 °C). The thermostability of K621F also exhibited a substantial improvement. Considering that the gelling temperature of the agarose is higher than 35 °C, K621F can be used to hydrolyze agarose for neoagarobiose production.

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Organizational Affiliation: 

Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B-agarase	A, B	765	Agarivorans gilvus	Mutation(s): 0
UniProt
Find proteins for A0A023LLI1 (Agarivorans gilvus) Explore A0A023LLI1  Go to UniProtKB:  A0A023LLI1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.245 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 215.801	α = 90
b = 93.647	β = 105.66
c = 85.049	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-01-24 
• Released Date: 2019-01-02 
Deposition Author(s): Mao, X., Zhou, J., Zhang, P., Zhang, L., Zhang, J., Li, Y.

Revision History  

• Version 1.0: 2019-01-02
  Type: Initial release
  
• Version 1.1: 2019-03-06
  Changes: Data collection, Database references