2CAV

CANAVALIN FROM JACK BEAN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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.,Sect.D 56: 411-420

  • DOI: 10.1107/s0907444900002237
  • Primary Citation of Related Structures:  

  • 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 sub ...

    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.


    Related Citations: 
    • The Three-Dimensional Structure of Canavalin from Jack Bean (Canavalia Ensiformis)
      Ko, T.-P.,Ng, J.D.,Macpherson, A.
      (1993) Plant Physiol. 101: 729


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CANAVALIN)
A
445Canavalia ensiformisMutation(s): 0 
Find proteins for P50477 (Canavalia ensiformis)
Go to UniProtKB:  P50477
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.208 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 126.430α = 90.00
b = 126.430β = 90.00
c = 51.370γ = 120.00
Software Package:
Software NamePurpose
SDMSdata reduction
SDMSdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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