6TAA

STRUCTURE AND MOLECULAR MODEL REFINEMENT OF ASPERGILLUS ORYZAE (TAKA) ALPHA-AMYLASE: AN APPLICATION OF THE SIMULATED-ANNEALING METHOD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.

Swift, H.J.Brady, L.Derewenda, Z.S.Dodson, E.J.Dodson, G.G.Turkenburg, J.P.Wilkinson, A.J.

(1991) Acta Crystallogr B 47: 535-544

  • DOI: 10.1107/s0108768191001970
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-70 ...

    Monoclinic crystals of a neutral alpha-amylase from Aspergillus oryzae, containing three molecules in the asymmetric unit, have been reported previously and studied at 3 A resolution [Matsuura, Kunusoki, Harada & Kakudo (1984). J. Biochem. 95, 697-702]. Here we report the solution of the structure of this enzyme in a different crystal form (space group P2(1)2(1)2(1), a = 50.9, b = 67.2, c = 132.7 A), with only one molecule in the asymmetric unit. The structure was solved by the molecular replacement method, using a model of acid alpha-amylase from a related fungus A. niger [Brady, Brzozowski, Derewenda, Dodson & Dodson (1991). Acta Cryst. B47, 527-535]. Conventional least-squares crystallographic refinement failed to converge in a satisfactory manner, and the technique of molecular dynamics in the form of the XPLOR package [Brunger (1988). XPLOR Manual. Yale Univ., USA] was used to overcome the problem. A large rigid-body type movement of the C-terminal domain was identified and accounted for. The final round of restrained least-squares refinement (at 2.1 A resolution) including 3675 protein atoms and 247 water molecules resulted in a conventional crystallographic R factor of 0.183 and an atomic model which conforms well to standard stereochemical parameters (standard deviation of bond lengths from their expected values is 0.028 A, while that for planar groups is 0.029 A).


    Related Citations: 
    • Calcium Binding in Alpha-Amylases: An X-Ray Diffraction Study at 2.1 Angstroms Resolution of Two Enzymes from Aspergillus
      Boel, E., Brady, L., Brzozowski, A.M., Derewenda, Z., Dodson, G.G., Jensen, V.J., Petersen, S.B., Swift, H., Thim, L., Woldike, H.F.
      (1990) Biochemistry 29: 6244

    Organizational Affiliation

    Department of Chemistry, University of York, Heslington, England.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-AMYLASEA478Aspergillus oryzaeMutation(s): 0 
EC: 3.2.1.1
Find proteins for P0C1B3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore P0C1B3 
Go to UniProtKB:  P0C1B3
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
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.04α = 90
b = 67.183β = 90
c = 133.56γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance