5BCA

BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.

Oyama, T.Kusunoki, M.Kishimoto, Y.Takasaki, Y.Nitta, Y.

(1999) J Biochem 125: 1120-1130

  • DOI: 10.1093/oxfordjournals.jbchem.a022394
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of beta-amylase from Bacillus cereus var. mycoides was determined by the multiple isomorphous replacement method. The structure was refined to a final R-factor of 0.186 for 102,807 independent reflections with F/sigma(F) > or = ...

    The crystal structure of beta-amylase from Bacillus cereus var. mycoides was determined by the multiple isomorphous replacement method. The structure was refined to a final R-factor of 0.186 for 102,807 independent reflections with F/sigma(F) > or = 2.0 at 2.2 A resolution with root-mean-square deviations from ideality in bond lengths, and bond angles of 0.014 A and 3.00 degrees, respectively. The asymmetric unit comprises four molecules exhibiting a dimer-of-dimers structure. The enzyme, however, acts as a monomer in solution. The beta-amylase molecule folds into three domains; the first one is the N-terminal catalytic domain with a (beta/alpha)8 barrel, the second one is the excursion part from the first one, and the third one is the C-terminal domain with two almost anti-parallel beta-sheets. The active site cleft, including two putative catalytic residues (Glu172 and Glu367), is located on the carboxyl side of the central beta-sheet in the (beta/alpha)8 barrel, as in most amylases. The active site structure of the enzyme resembles that of soybean beta-amylase with slight differences. One calcium ion is bound per molecule far from the active site. The C-terminal domain has a fold similar to the raw starch binding domains of cyclodextrin glycosyltransferase and glucoamylase.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of Beta-Amylase from Bacillus Cereus Var. Mycoides
      Oyama, T., Kusunoki, M., Kishimoto, Y., Takasaki, Y., Nitta, Y.
      (1998) Protein Pept Lett 5: 349
    • Kinetic Study of Active Site Structure of Beta-Amylase from Bacillus Cereus Var. Mycoides
      Nitta, Y., Shirakawa, M., Takasaki, Y.
      (1996) Biosci Biotechnol Biochem 60: 823
    • Cloning, Sequencing, and Expression of a Beta-Amylase Gene from Bacillus Cereus Var. Mycoides and Characterization of its Products
      Yamaguchi, T., Matsumoto, Y., Shirakawa, M., Kibe, M., Hibino, T., Kozaki, S., Takasaki, Y., Nitta, Y.
      (1996) Biosci Biotechnol Biochem 60: 1255

    Organizational Affiliation

    Laboratory of Enzyme Chemistry, College of Agriculture, University of Osaka Prefecture, Sakai, Osaka, 599-8531, Japan. chicago@biochem. osakafu-u.ac.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)A, B, C, D516Bacillus cereusMutation(s): 0 
Gene Names: spoII
EC: 3.2.1.2
Find proteins for P36924 (Bacillus cereus)
Explore P36924 
Go to UniProtKB:  P36924
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.9α = 90
b = 112.9β = 105.8
c = 146.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-03-15
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance