Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 

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This is version 1.5 of the entry. See complete history


Crystal structure of Bacillus stearothermophilus alpha-amylase: possible factors determining the thermostability.

Suvd, D.Fujimoto, Z.Takase, K.Matsumura, M.Mizuno, H.

(2001) J Biochem 129: 461-468

  • DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a002878
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of a thermostable alpha-amylase from Bacillus stearothermophilus (BSTA) has been determined at 2.0 A resolution. The main-chain fold is almost identical to that of the known crystal structure of Bacillus licheniformis alpha-amylase (BLA). BLA is known to be more stable than BSTA. A structural comparison between the crystal structures of BSTA and BLA showed significant differences that may account for the difference in their thermostabilities, as follows. (i) The two-residue insertion in BSTA, Ile181-Gly182, pushes away the spatially contacting region including Asp207, which corresponds to Ca(2+)-coordinating Asp204 in BLA. As a result, Asp207 cannot coordinate the Ca(2+). (ii) BSTA contains nine fewer hydrogen bonds than BLA, which costs about 12 kcal/mol. This tendency is prominent in the (beta/alpha)(8)-barrel, where 10 fewer hydrogen bonds were observed in BSTA. BLA forms a denser hydrogen bond network in the inter-helical region, which may stabilize alpha-helices in the barrel. (iii) A few small voids observed in the alpha-helical region of the (beta/alpha)(8)-barrel in BSTA decrease inter-helical compactness and hydrophobic interactions. (iv) The solvent-accessible surface area of charged residues in BLA is about two times larger than that in BSTA.

  • Organizational Affiliation

    Institute of Applied Biochemistry, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan. mizuno@abr.affrc.go.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-AMYLASE515Geobacillus stearothermophilusMutation(s): 0 
Gene Names: AMYT631
Find proteins for P06279 (Geobacillus stearothermophilus)
Explore P06279 
Go to UniProtKB:  P06279
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06279
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.55α = 90
b = 93.119β = 109.31
c = 53.275γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-01-31
    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: 2012-02-15
    Changes: Database references
  • Version 1.4: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.5: 2024-03-13
    Changes: Data collection, Database references, Derived calculations