9JP3 | pdb_00009jp3

COMPLEX STRUCTURE OF ENDO-1,3-FUCANASE MUTANT D171A WITH FUCOTETRAOSE

• PDB DOI: https://doi.org/10.2210/pdb9JP3/pdb

• Classification: HYDROLASE
• Organism(s): Novipirellula artificiosorum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-09-25 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: 
  0.174 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.157 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: in silico

Literature

Complex structure of endo-1.3-fucanase mutant D171A with fucotetraose at 1.40 Angstroms resulution.

Chen, G.N., Chang, Y.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.65 kDa 
• Atom Count: 3,492 
• Modelled Residue Count: 360 
• Deposited Residue Count: 409 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoside-hydrolase family GH114 TIM-barrel domain-containing protein	A	409	Novipirellula artificiosorum	Mutation(s): 1  Gene Names: Poly41_55130
UniProt
Find proteins for A0A5C6D8T6 (Novipirellula artificiosorum) Explore A0A5C6D8T6  Go to UniProtKB:  A0A5C6D8T6

Oligosaccharides

Help

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.174 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.157 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.782	α = 90
b = 152.782	β = 90
c = 42.337	γ = 120

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