Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 111.01 kDa 
• Atom Count: 8295 
• Modelled Residue Count: 962 
• Deposited Residue Count: 962 
• Unique protein chains: 1

1QVB

CRYSTAL STRUCTURE OF THE BETA-GLYCOSIDASE FROM THE HYPERTHERMOPHILE THERMOSPHAERA AGGREGANS

• PDB DOI: 10.2210/pdb1QVB/pdb

• Classification: HYDROLASE
• Organism(s): Thermosphaera aggregans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-07-07 Released: 1999-07-13 
• Deposition Author(s): Chi, Y.-I., Martinez-Cruz, L.A., Swanson, R.V., Robertson, D.E., Kim, S.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.210 
• R-Value Observed: 0.217 

Literature

Crystal structure of the beta-glycosidase from the hyperthermophile Thermosphaera aggregans: insights into its activity and thermostability.

Chi, Y.I., Martinez-Cruz, L.A., Jancarik, J., Swanson, R.V., Robertson, D.E., Kim, S.H.

(1999) FEBS Lett 445: 375-383

• PubMed: 10094493 
• DOI: 10.1016/s0014-5793(99)00090-3
• Primary Citation of Related Structures:  
  1QVB


• PubMed Abstract: 
  

The glycosyl hydrolases are an important group of enzymes that are responsible for cleaving a range of biologically significant carbohydrate compounds. Structural information on these enzymes has provided useful information on their molecular basis for the functional variations, while the characterization of the structural features that account for the high thermostability of proteins is of great scientific and biotechnological interest. To these ends we have determined the crystal structure of the beta-glycosidase from a hyperthermophilic archeon Thermosphaera aggregans. The structure is a (beta/alpha)8 barrel (TIM-barrel), as seen in other glycosyl hydrolase family 1 members, and forms a tetramer. Inspection of the active site and the surrounding area reveals two catalytic glutamate residues consistent with the retaining mechanism and the surrounding polar and aromatic residues consistent with a monosaccharide binding site. Comparison of this structure with its mesophilic counterparts implicates a variety of structural features that could contribute to the thermostability. These include an increased number of surface ion pairs, an increased number of internal water molecules and a decreased surface area upon forming an oligomeric quaternary structure.

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Organizational Affiliation: 

Department of Chemistry and Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLYCOSIDASE	A, B	481	Thermosphaera aggregans	Mutation(s): 0
UniProt
Find proteins for Q9YGA8 (Thermosphaera aggregans) Explore Q9YGA8  Go to UniProtKB:  Q9YGA8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.210 
• R-Value Observed: 0.217 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.509	α = 90
b = 102.215	β = 90
c = 95.776	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-07 
• Released Date: 1999-07-13 
Deposition Author(s): Chi, Y.-I., Martinez-Cruz, L.A., Swanson, R.V., Robertson, D.E., Kim, S.-H.

Revision History  

• Version 1.0: 1999-07-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection