1KJ1

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Re-refinement using reprocessed data to improve the quality of the structure: a case study involving garlic lectin.

Ramachandraiah, G.Chandra, N.R.Surolia, A.Vijayan, M.

(2002) Acta Crystallogr.,Sect.D 58: 414-420


  • PubMed Abstract: 
  • The structure of dimeric garlic lectin was previously determined to an effective resolution of 2.8A using X-ray intensity data processed by the XDS package and refined using X-PLOR [Chandra et al. (1999), J. Mol. Biol. 285, 1157--1168]. Repeated atte ...

    The structure of dimeric garlic lectin was previously determined to an effective resolution of 2.8A using X-ray intensity data processed by the XDS package and refined using X-PLOR [Chandra et al. (1999), J. Mol. Biol. 285, 1157--1168]. Repeated attempts to grow better crystals with a view to improving the definition of the structure did not succeed. The available raw data were then reprocessed using DENZO. The structure was re-refined with both X-PLOR and CNS separately using the reprocessed data, which extended to a resolution of 2.2A. These two sets of refinements and the two sets using the XDS-processed data afforded an opportunity to compare the performance of different data-processing and refinement packages when dealing with data from weakly diffracting crystals. The best results were obtained when CNS was employed for refinement using data processed by DENZO. The quality and the resolution of the map and the definition of the structure improved substantially. In particular, the amino-acid residues at the variable locations in the sequence, and hence the isolectins, could be identified with a high degree of confidence. It could be established that the crystal asymmetric unit contains two identical heterodimers. The new refined structure also provided a better definition of other finer structural details.


    Related Citations: 
    • Crystal Structure of a Dimeric Mannose-Specific Agglutinin from Garlic: Quaternary Association and Carbohydrate Specificity
      Chandra, N.R.,Ramachandraiah, G.,Bachhawat, K.,Dam, T.K.,Surolia, A.,Vijayan, M.
      (1999) J.Mol.Biol. 285: 1157
    • Crystallization and Preliminary Crystallographic Studies on the Mannose-Specific Lectin from Garlic
      Chandra, N.R.,Dam, T.K.,Surolia, A.,Vijayan, M.
      (1997) Acta Crystallogr.,Sect.D 53: 787


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
lectin I
A, P
109Allium sativumGene Names: LECASAI3
Find proteins for Q38789 (Allium sativum)
Go to UniProtKB:  Q38789
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
lectin II
D, Q
109Allium sativumGene Names: ASAII1
Find proteins for Q38783 (Allium sativum)
Go to UniProtKB:  Q38783
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, D, P, Q
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 201.831α = 90.00
b = 43.516β = 112.26
c = 78.736γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance