5YGM

Monomeric structure of concanavalin A at pH 7.5 from Carnivalia ensiformis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Heterometal-Coordinated Monomeric Concanavalin A at pH 7.5 from Canavalia ensiformis

Chung, N.J., Park, Y.R., Lee, D.H., Oh, S.Y., Park, J.H., Lee, S.J.

(2017) J Microbiol Biotechnol 27: 2241-2244

  • DOI: https://doi.org/10.4014/jmb.1709.09057
  • Primary Citation of Related Structures:  
    5YGM

  • PubMed Abstract: 

    The structure of concanavalin A (ConA) has been studied intensively owing to its specific interactions with carbohydrates and its heterometal (Ca²⁺ and Mn²⁺) coordination. Most structures from X-ray crystallography have shown ConA as a dimer or tetramer, because the complex formation requires specific crystallization conditions. Here, we reported the monomeric structure of ConA with a resolution of 1.6 Å, which revealed that metal coordination could trigger sugar-binding ability. The calcium coordination residue, Asn14, changed the orientation of carbohydrate-binding residues and biophysical details, including structural information, providing valuable clues for the development and application of detection kits using ConA.

    • Organizational Affiliation: 

    Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, Republic of Korea.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Concanavalin-A237Canavalia ensiformisMutation(s): 0 
UniProt
Find proteins for P55915 (Canavalia brasiliensis)
Explore P55915 
Go to UniProtKB:  P55915
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55915
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.303α = 90
b = 86.59β = 90
c = 89.511γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata processing
SCALAdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cooperative Research Program for Agriculture Science and Technology Development Rural Development AdministrationKorea, Republic OfPJ011067

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-25
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2018-08-01
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.3: 2018-08-15
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description