9JOG | pdb_00009jog

COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE (FUN168D) WITH FUCOTETRAOSE FROM HOLOTHURIA TUBULOSA

• PDB DOI: https://doi.org/10.2210/pdb9JOG/pdb

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


• Deposited: 2024-09-24 Released: 2024-11-27 
• Deposition Author(s): Chen, G.N., Chang, Y.G.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.155 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.140 (Depositor), 0.147 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Starting Model: in silico

Literature

Complex structure of endo-1.3-fucanase (Fun168D) with fucotetraose from Holothuria tubulosa at 1.40 Angstroms resulution.

Chen, G.N., Chang, Y.G.

To be published.

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 (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 97.86 kDa 
• Atom Count: 7,488 
• Modelled Residue Count: 738 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endo-1.3-fucanase	A, B	423	Wenyingzhuangia fucanilytica	Mutation(s): 0  Gene Names: AXE80_08865
UniProt
Find proteins for A0A1B1Y6G8 (Wenyingzhuangia fucanilytica) Explore A0A1B1Y6G8  Go to UniProtKB:  A0A1B1Y6G8

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2,4-di-O-sulfo-alpha-L-fucopyranose-(1-3)-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose-(1-3)-2-O-sulfo-alpha-L-fucopyranose	C, D	4	N/A	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.155 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.140 (Depositor), 0.147 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.741	α = 90
b = 138.39	β = 113.66
c = 62.866	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-27 
Deposition Author(s): Chen, G.N., Chang, Y.G.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	U22A20542

Revision History  

• Version 1.0: 2024-11-27
  Type: Initial release