1KJ1

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

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This is version 1.3 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 D Biol Crystallogr 58: 414-420

  • DOI: https://doi.org/10.1107/s0907444901021497
  • Primary Citation of Related Structures:  
    1KJ1

  • 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 attempts to grow better crystals with a view to improving the definition of the structure did not succeed ...

    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 D Biol Crystallogr 53: 787
    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
lectin IA,
C [auth P]		109Allium sativumMutation(s): 0 
Gene Names: LECASAI3
UniProt
Find proteins for Q38789 (Allium sativum)
Explore Q38789 
Go to UniProtKB:  Q38789
Entity Groups  
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UniProt GroupQ38789
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
lectin IIB [auth D],
D [auth Q]		109Allium sativumMutation(s): 0 
Gene Names: ASAII1
UniProt
Find proteins for Q38783 (Allium sativum)
Explore Q38783 
Go to UniProtKB:  Q38783
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ38783
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.831α = 90
b = 43.516β = 112.26
c = 78.736γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary