1GYD

Structure of Cellvibrio cellulosa alpha-L-arabinanase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cellvibrio japonicus alpha-L-arabinanase 43A has a novel five-blade beta-propeller fold.

Nurizzo, D.Turkenburg, J.P.Charnock, S.J.Roberts, S.M.Dodson, E.J.McKie, V.A.Taylor, E.J.Gilbert, H.J.Davies, G.J.

(2002) Nat Struct Biol 9: 665-668

  • DOI: https://doi.org/10.1038/nsb835
  • Primary Citation of Related Structures:  
    1GYD, 1GYE, 1GYH

  • PubMed Abstract: 

    Cellvibrio japonicus arabinanase Arb43A hydrolyzes the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The three-dimensional structure of Arb43A, determined at 1.9 A resolution, reveals a five-bladed beta-propeller fold. Arb43A is the first enzyme known to display this topology. A long V-shaped surface groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Three carboxylates deep in the active site groove provide the general acid and base components for glycosidic bond hydrolysis with inversion of anomeric configuration.


  • Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ARABINAN ENDO-1,5-ALPHA-L-ARABINOSIDASE AA [auth B]315Cellvibrio japonicusMutation(s): 0 
EC: 3.2.1.99
UniProt
Find proteins for P95470 (Cellvibrio japonicus (strain Ueda107))
Explore P95470 
Go to UniProtKB:  P95470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP95470
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.078α = 90
b = 90.078β = 90
c = 177.217γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-02-28
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Other, Refinement description