5BCA

BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 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.(Tokyo) 125: 1120-1130


  • 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: 
    • 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
    • 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
    • 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, D
516Bacillus cereusGene Names: spoII
EC: 3.2.1.2
Find proteins for P36924 (Bacillus cereus)
Go to UniProtKB:  P36924
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
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: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 177.900α = 90.00
b = 112.900β = 105.80
c = 146.200γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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