3IPV

Crystal structure of Spatholobus parviflorus seed lectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

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This is version 1.3 of the entry. See complete history


Literature

X-ray structure of a galactose-specific lectin from Spatholobous parviflorous

Geethanandan, K.Abhilash, J.Bharath, S.R.Sadasivan, C.Haridas, M.

(2011) Int J Biol Macromol 49: 992-998

  • DOI: https://doi.org/10.1016/j.ijbiomac.2011.08.021
  • Primary Citation of Related Structures:  
    3IPV

  • PubMed Abstract: 

    A galactose-specific seed lectin from Spatholobous parviflorus (SPL) has been purified, crystallized and its X-ray structure solved. It is the first lectin purified and crystallized from the genus Spatholobus (family: Fabaceae). The crystals belong to the space group P1, with a=60.792 Å, b=60.998 Å, c=78.179 Å, α=78.68°, β=88.62°, γ=104.32°. The data were collected at 2.04 Å resolution under cryocondition, on a MAR image-plate detector system, mounted on a rotating anode X-ray generator. The coordinates of Dolichos biflorus lectin (1lu1) were successfully used for the structure solution by molecular replacement method. The primary structure of the SPL was not known earlier and it was unambiguously visible in the electron density. S. parviflorus lectin is a hetero-dimeric-tetramer with two alpha and two beta chains of 251 and 239 residues respectively. SPL has two metal ions, Ca(2+) and Mn(2+), bound to a loop region of each chain. The SPL monomers are in jelly roll form.


  • Organizational Affiliation

    Department of Biotechnology and Microbiology, Kannur University, Thalassery Campus, 670661 Kerala, India.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin alpha chain
A, C
251Spatholobus parviflorusMutation(s): 0 
UniProt
Find proteins for P86352 (Spatholobus parviflorus)
Explore P86352 
Go to UniProtKB:  P86352
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP86352
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Lectin beta chain
B, D
239Spatholobus parviflorusMutation(s): 0 
UniProt
Find proteins for P86353 (Spatholobus parviflorus)
Explore P86353 
Go to UniProtKB:  P86353
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP86353
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.04 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.998α = 101.32
b = 60.792β = 91.38
c = 78.179γ = 104.32
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2012-02-15
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description