8YFH | pdb_00008yfh

Structure of alpha-1,3-glucanase agn1

• PDB DOI: https://doi.org/10.2210/pdb8YFH/pdb

• Classification: HYDROLASE
• Organism(s): Schizosaccharomyces pombe DM3650
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-24 Released: 2025-02-26 
• Deposition Author(s): Horaguch, Y., Yano, S., Makabe, K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: in silico

Literature

Structure of alpha-1,3-glucanase agn1

Horaguchi, Y., Yano, S., Makabe, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 133.6 kDa 
• Atom Count: 10,621 
• Modeled Residue Count: 1,206 
• Deposited Residue Count: 1,206 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucan endo-1,3-alpha-glucosidase agn1	A, B, C	402	Schizosaccharomyces pombe DM3650	Mutation(s): 0  Gene Names: agn1, SPAC14C4.09 EC: 3.2.1.59
UniProt
Find proteins for O13716 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O13716  Go to UniProtKB:  O13716

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.534	α = 90
b = 114.514	β = 104.236
c = 109.111	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-26 
Deposition Author(s): Horaguch, Y., Yano, S., Makabe, K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-26
  Type: Initial release