5J76

Structure of Lectin from Colocasia esculenta(L.) Schott


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural analysis of beta-prism lectin from Colocasia esculenta (L.) S chott.

Vajravijayan, S.Pletnev, S.Pletnev, V.Z.Nandhagopal, N.Gunasekaran, K.

(2016) Int.J.Biol.Macromol. 91: 518-523

  • DOI: 10.1016/j.ijbiomac.2016.05.048

  • PubMed Abstract: 
  • The Mannose-binding β-Prism Colocasia esculenta lectin (β-PCL) was purified from tubers using ion exchange chromatography. The purified β-PCL appeared as a single band of ∼12kDa on SDS-PAGE. β-PCL crystallizes in trigonal space group P3121 and diffra ...

    The Mannose-binding β-Prism Colocasia esculenta lectin (β-PCL) was purified from tubers using ion exchange chromatography. The purified β-PCL appeared as a single band of ∼12kDa on SDS-PAGE. β-PCL crystallizes in trigonal space group P3121 and diffracted to a resolution of 2.1Å. The structure was solved using Molecular replacement using Crocus vernus lectin (PDB: 3MEZ) as a model. From the final refined model to an R-factor of 16.5% and an Rfree of 20.4%, it has been observed that the biological unit consists of two β-Prism domains augmented through C-terminals swap over to form one of faces for each domain. Cα superposition of individual domains of β-PCL with individual domains of other related structures and superposition of whole protein structures were carried out. The higher RMS deviation for the superposition of whole structures suggest that β-prism domains assume different orientation in each structure.


    Organizational Affiliation

    Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
12kD storage protein
A
109Colocasia esculentaMutation(s): 0 
Find proteins for Q39487 (Colocasia esculenta)
Go to UniProtKB:  Q39487
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
12kD storage protein
B
111Colocasia esculentaMutation(s): 0 
Find proteins for Q39487 (Colocasia esculenta)
Go to UniProtKB:  Q39487
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.471α = 90.00
b = 75.471β = 90.00
c = 121.177γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-06-29
    Type: Database references