Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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This is version 1.3 of the entry. See complete history


The refined structure of canavalin from jack bean in two crystal forms at 2.1 and 2.0 A resolution.

Ko, T.P.Day, J.McPherson, A.

(2000) Acta Crystallogr D Biol Crystallogr 56: 411-420

  • DOI: https://doi.org/10.1107/s0907444900002237
  • Primary Citation of Related Structures:  
    2CAU, 2CAV

  • PubMed Abstract: 

    The structure of canavalin was refined to 2.1 and 2.0 A resolution in cubic and hexagonal crystals of space group P2(1)3 and P6(3), respectively. The threefold molecular symmetry is expressed in the symmetry of both crystals, where each identical subunit is an asymmetric unit. The canavalin subunit consists of two very similar domains, each comprised of a core subdomain having Swiss-roll topology with a loop subdomain that contains helices. The refined canavalin models resolved the discrepancy in amino-acid registers of the secondary-structural elements compared with phaseolin. The presence of strand Z in both domains of canavalin was confirmed and a new helix in the loop between strands A and B of each domain was observed. The models were analyzed in terms of the duplicated vicilin domains. Three strictly conserved residues, two glycines and a proline, were identified. The similarity between entire vicilin molecules is greater than that between separate domains of canavalin and phaseolin. Homology modeling of the sucrose-binding protein (SBP) from soybean showed a plausible trimeric assembly of subunits similar to that of vicilins.

  • Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (CANAVALIN)445Canavalia ensiformisMutation(s): 0 
Find proteins for P50477 (Canavalia ensiformis)
Explore P50477 
Go to UniProtKB:  P50477
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50477
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.43α = 90
b = 126.43β = 90
c = 51.37γ = 120
Software Package:
Software NamePurpose
SDMSdata reduction
SDMSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-25
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description