1WBF

WINGED BEAN LECTIN, SACCHARIDE FREE FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.197 

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This is version 1.3 of the entry. See complete history


Literature

Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.

Manoj, N.Srinivas, V.R.Suguna, K.

(1999) Acta Crystallogr D Biol Crystallogr 55: 794-800

  • DOI: 10.1107/s090744499900044x
  • Primary Citation of Related Structures:  
    1WBF

  • PubMed Abstract: 
  • The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 A resolution. The final R factor is 19.7% for all data in the resolution range 8.0-2 ...

    The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 A resolution. The final R factor is 19.7% for all data in the resolution range 8.0-2.3 A. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI with methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures. The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which are hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 A of the main-chain atoms of the variable loop.


    Related Citations: 
    • Carbohydrate Specificity and Quaternary Association in Basic Winged Bean Lectin: X-Ray Analysis of the Lectin at 2.5 A Resolution
      Prabu, M.M., Sankaranarayanan, R., Puri, K.D., Sharma, V., Surolia, A., Vijayan, M., Suguna, K.
      (1998) J Mol Biol 276: 787
    • Crystallization and Preliminary X-Ray Studies of the Basic Lectin from Winged Bean (Psophocarpus Tetragonolobus)
      Sankaranarayanan, R., Puri, K.D., Ganesh, V., Banerjee, R., Surolia, A., Vijayan, M.
      (1993) J Mol Biol 229: 558

    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560 012, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (AGGLUTININ)A, B242Psophocarpus tetragonolobusMutation(s): 0 
Gene Names: WBAI
UniProt
Find proteins for O24313 (Psophocarpus tetragonolobus)
Explore O24313 
Go to UniProtKB:  O24313
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO24313
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.159α = 90
b = 75.161β = 106.91
c = 95.772γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary