5GHL

Crystal structure Analysis of the starch-binding domain of glucoamylase from Aspergillus niger


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the starch-binding domain of glucoamylase from Aspergillus niger.

Suyama, Y.Muraki, N.Kusunoki, M.Miyake, H.

(2017) Acta Crystallogr F Struct Biol Commun 73: 550-554

  • DOI: https://doi.org/10.1107/S2053230X17012894
  • Primary Citation of Related Structures:  
    5GHL

  • PubMed Abstract: 

    Glucoamylases are widely used commercially to produce glucose syrup from starch. The starch-binding domain (SBD) of glucoamylase from Aspergillus niger is a small globular protein containing a disulfide bond. The structure of A. niger SBD has been determined by NMR, but the conformation surrounding the disulfide bond was unclear. Therefore, X-ray crystal structural analysis was used to attempt to clarify the conformation of this region. The SBD was purified from an Escherichia coli-based expression system and crystallized at 293 K. The initial phase was determined by the molecular-replacement method, and the asymmetric unit of the crystal contained four protomers, two of which were related by a noncrystallographic twofold axis. Finally, the structure was solved at 2.0 Å resolution. The SBD consisted of seven β-strands and eight loops, and the conformation surrounding the disulfide bond was determined from a clear electron-density map. Comparison of X-ray- and NMR-determined structures of the free SBD showed no significant difference in the conformation of each β-strand, but the conformations of the loops containing the disulfide bond and the L5 loop were different. In particular, the difference in the position of the C α atom of Cys509 between the X-ray- and NMR-determined structures was 13.3 Å. In addition, the B factors of the amino-acid residues surrounding the disulfide bond are higher than those of other residues. Therefore, the conformation surrounding the disulfide bond is suggested to be highly flexible.


  • Organizational Affiliation

    Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu, Mie 514-8507, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucoamylase
A, B, C, D
108Aspergillus nigerMutation(s): 0 
Gene Names: GLAA
EC: 3.2.1.3
UniProt
Find proteins for P69328 (Aspergillus niger)
Explore P69328 
Go to UniProtKB:  P69328
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP69328
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.36α = 90
b = 75.36β = 90
c = 91.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-18
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description