2ZBJ

Crystal structure of Dioclea rostrata lectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of Dioclea rostrata lectin: Insights into understanding the pH-dependent dimer-tetramer equilibrium and the structural basis for carbohydrate recognition in Diocleinae lectins

de Oliveira, T.M.Delatorre, P.da Rocha, B.A.M.de Souza, E.P.Nascimento, K.S.Bezerra, G.A.Moura, T.R.Benevides, R.G.Bezerra, E.H.S.Moreno, F.B.M.B.Freire, V.N.de Azevedo Jr., W.F.Cavada, B.S.

(2008) J Struct Biol 164: 177-182

  • DOI: https://doi.org/10.1016/j.jsb.2008.05.012
  • Primary Citation of Related Structures:  
    2ZBJ

  • PubMed Abstract: 

    The legume lectins from the subtribe Diocleinae, often referred to as concanavalin A-like lectins, are a typical example of highly similar proteins that show distinct biological activities. The pH-dependent oligomerization that some of these lectins undergo and the relative position of amino acids within the carbohydrate-binding site are factors that have been reported to contribute to these differences in the activities of Diocleinae lectins. In the present work, we determined the amino acid sequence and the crystal structure of the lectin of Dioclea rostrata seeds (DRL), with the aim of investigating the structural bases of the different behavior displayed by this lectin in comparison to other Diocleinae lectins and determining the reason for the distinct pH-dependent dimer-tetramer equilibrium. In addition, we discovered a novel multimeric arrangement for this lectin.


  • Organizational Affiliation

    Federal University of Ceará, Departmento Biochemistry and Molecular Biology, Campus do Pici s/n Caixa Postal 6043, 60455-970 Fortaleza, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin alpha chain237Macropsychanthus bicolorMutation(s): 0 
UniProt
Find proteins for P58908 (Macropsychanthus bicolor)
Explore P58908 
Go to UniProtKB:  P58908
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58908
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.511α = 90
b = 88.22β = 90
c = 87.764γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description