Crystal structure analysis of NP24-I, a thaumatin-like protein

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

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Crystal structure analysis of NP24-I: a thaumatin-like protein

Ghosh, R.Chakrabarti, C.

(2008) Planta 228: 883-890

  • DOI: https://doi.org/10.1007/s00425-008-0790-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of NP24-I, an isoform of the thaumatin-like protein (TLP) NP24 from tomato, has been reported. A prominent acidic cleft is observed between domains I and II of the three-domain structure of this antifungal protein, a feature common to other antifungal TLPs. The defensive role of the TLPs has also been attributed to their beta-1,3-glucanase activity and here too the acidic cleft is reported to play a vital role. NP24 is known to bind beta-glucans and so a linear beta-1,3-glucan molecule has been docked in the interdomain cleft of NP24-I. From the docked complex it is observed that the beta-glucan chain is so positioned in the cleft that a Glu and Asp residue on either side of it may form a catalytic pair to cause the cleavage of a glycosidic bond. NP24 has been reported to be an allergenic protein and an allergenic motif could be identified on the surface of the helical domain II of NP24-I. In addition, some allergenic motifs bearing high similarity/identity with some predicted Ig-E binding motifs of closely related allergenic TLPs like Jun a 3 (Juniperus ashei, from mountain cedar pollen) and banana-TLP have been identified on the molecular surface of NP24-I.

  • Organizational Affiliation

    Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700 064, India.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NP24207Solanum lycopersicumMutation(s): 0 
Find proteins for P12670 (Solanum lycopersicum)
Explore P12670 
Go to UniProtKB:  P12670
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12670
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CL

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.01α = 90
b = 61.01β = 90
c = 62.895γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
AUTOMARdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description