Crystal structure of calcium free alpha amylase from Bacillus sp. strain KSM-K38 (AmyK38, in calcium containing solution)

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 

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Crystal structure of calcium-free alpha-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites

Nonaka, T.Fujihashi, M.Kita, A.Hagihara, H.Ozaki, K.Ito, S.Miki, K.

(2003) J Biol Chem 278: 24818-24824

  • DOI: https://doi.org/10.1074/jbc.M212763200
  • Primary Citation of Related Structures:  
    1UD2, 1UD3, 1UD4, 1UD5, 1UD6, 1UD8

  • PubMed Abstract: 

    The crystal structure of a calcium-free alpha-amylase (AmyK38) from Bacillus sp. strain KSM-K38, which resists chelating reagents and chemical oxidants, has been determined by the molecular replacement method and refined to a crystallographic R-factor of 19.9% (R-free of 23.2%) at 2.13-A resolution. The main chain folding of AmyK38 is almost homologous to that of Bacillus licheniformis alpha-amylase. However, neither a highly conserved calcium ion, which is located at the interface between domains A and B, nor any other calcium ions appear to exist in the AmyK38 molecule, although three sodium ions were found, one of which is located at the position corresponding to that of a highly conserved calcium ion of other alpha-amylases. The existence of these sodium ions was crystallographically confirmed by the structures of three metal-exchanged and mutated enzymes. This is the first case in which the structure of the calcium-free alpha-amylase has been determined by crystallography, and it was suggested that these sodium ions, instead of calcium ions, are used to retain the structure and function of AmyK38.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
amylase480Bacillus sp. KSM-K38Mutation(s): 0 
Find proteins for Q93I48 (Bacillus sp. KSM-K38)
Explore Q93I48 
Go to UniProtKB:  Q93I48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93I48
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.192 
  • Space Group: P 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.731α = 90
b = 133.731β = 90
c = 133.731γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-22
    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: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description