Document Detail


Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.
MedLine Citation:
PMID:  1930835     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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).
Authors:
H J Swift; L Brady; Z S Derewenda; E J Dodson; G G Dodson; J P Turkenburg; A J Wilkinson
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Acta crystallographica. Section B, Structural science     Volume:  47 ( Pt 4)     ISSN:  0108-7681     ISO Abbreviation:  Acta Crystallogr., B     Publication Date:  1991 Aug 
Date Detail:
Created Date:  1991-12-17     Completed Date:  1991-12-17     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  8403252     Medline TA:  Acta Crystallogr B     Country:  DENMARK    
Other Details:
Languages:  eng     Pagination:  535-44     Citation Subset:  IM    
Affiliation:
Department of Chemistry, University of York, Heslington, England.
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MeSH Terms
Descriptor/Qualifier:
Aspergillus oryzae / enzymology*
Chemistry, Physical
Crystallization
Models, Molecular*
Molecular Structure
Physicochemical Phenomena
Software
X-Ray Diffraction
alpha-Amylases / chemistry*
Chemical
Reg. No./Substance:
EC 3.2.1.1/alpha-Amylases

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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