4FNT

Crystal structure of GH36 alpha-galactosidase AgaA A355E D548N from Geobacillus stearothermophilus in complex with raffinose

• PDB DOI: https://doi.org/10.2210/pdb4FNT/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-06-20 Released: 2012-10-03 
• Deposition Author(s): Merceron, R., Foucault, M., Haser, R., Mattes, R., Watzlawick, H., Gouet, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 334.84 kDa 
• Atom Count: 23,619 
• Modelled Residue Count: 2,872 
• Deposited Residue Count: 2,916 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase AgaA	A, B, C, D	729	Geobacillus stearothermophilus	Mutation(s): 3  Gene Names: agaA EC: 3.2.1.22
UniProt
Find proteins for Q9ALJ4 (Geobacillus stearothermophilus) Explore Q9ALJ4  Go to UniProtKB:  Q9ALJ4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose	E, F, G	3		N/A
Glycosylation Resources
GlyTouCan:  G40178VU GlyCosmos:  G40178VU

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900002	E, F, G	raffinose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.221 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.68	α = 90
b = 149.68	β = 90
c = 234.77	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
PHENIX	refinement
XSCALE	data scaling
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Merceron, R., Foucault, M., Haser, R., Mattes, R., Watzlawick, H., Gouet, P.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2013-02-20
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary