2ZE0

Alpha-glucosidase GSJ

• PDB DOI: https://doi.org/10.2210/pdb2ZE0/pdb

• Classification: HYDROLASE
• Organism(s): Geobacillus sp. HTA-462
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2007-12-04 Released: 2007-12-18 
• Deposition Author(s): Shirai, T., Hung, V.S., Morinaka, K., Kobayashi, T., Ito, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 

Starting Model: experimental

Literature

Crystal structure of GH13 alpha-glucosidase GSJ from one of the deepest sea bacteria

Shirai, T., Hung, V.S., Morinaka, K., Kobayashi, T., Ito, S.

(2008) Proteins 73: 126-133

• PubMed: 18398906 
• DOI: https://doi.org/10.1002/prot.22044
• Primary Citation of Related Structures:  
  2ZE0


• PubMed Abstract: 
  

  The crystal structure of the GH13 alpha-glucosidase (GSJ) from deep-sea bacterium Geobacillus sp. strain HTA-462 was determined to a 2.0 A resolution. Comparisons of the GSJ structure with that of other GH13 enzymes with different catalytic activities revealed that the catalytic cleft of GSJ was widely opened when compared with the homologues. The wide opening of the catalytic cleft originated from conformational changes of active site residues and disorder of the regions close to the catalytic center. This structural feature of GSJ would explain the ability of this enzyme to accept a wide variety of nonsugar molecules as acceptors in the transglycosylation reaction.

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Organizational Affiliation: 

Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama 526-0829, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.3 kDa 
• Atom Count: 4,653 
• Modelled Residue Count: 531 
• Deposited Residue Count: 555 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A	555	Geobacillus sp. HTA-462	Mutation(s): 0  Gene Names: gsj EC: 3.2.1.20 (PDB Primary Data), 3.2.1.1 (UniProt)
UniProt
Find proteins for Q33E90 (Geobacillus sp. HTA-462) Explore Q33E90  Go to UniProtKB:  Q33E90

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.202 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.829	α = 90
b = 90.621	β = 109.4
c = 72.285	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Shirai, T., Hung, V.S., Morinaka, K., Kobayashi, T., Ito, S.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description