Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 

Starting Model: experimental
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Crystal structure of tobacco PR-5d protein at 1.8 A resolution reveals a conserved acidic cleft structure in antifungal thaumatin-like proteins.

Koiwa, H.Kato, H.Nakatsu, T.Oda, J.Yamada, Y.Sato, F.

(1999) J Mol Biol 286: 1137-1145

  • DOI: https://doi.org/10.1006/jmbi.1998.2540
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of tobacco PR-5d, an antifungal thaumatin-like protein isolated from cultured tobacco cells, was determined at the resolution of 1.8 A. The structure consists of 208 amino acid residues and 89 water molecules with a crystallographic R-factor of 0.169. The model has good stereochemistry, with respective root-mean-square deviations from the ideal values for bond and angle distances of 0.007 A and 1.542 degrees. Of the homologous PR-5 proteins, only those with antifungal activity had a common motif, a negatively charged surface cleft. This cleft is at the boundary between domains I and II, with a bottom part consisting of a three-stranded antiparallel beta-sheet in domain I. The acidic residues located in the hollow of the cleft form the beta-sheet region. Sequence and secondary structure analyses showed that the amino acid residues comprising the acidic cleft of PR-5d are conserved among other antifungal PR-5 proteins. This is the first report on the high-resolution crystal structure of an antifungal PR-5 protein. This structure provides insight into the function of pathogenesis-related proteins.

  • Organizational Affiliation

    Faculty of Agriculture, Kyoto University, Kyoto 606-8502, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PR-5D208Nicotiana tabacumMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P25871 (Nicotiana tabacum)
Explore P25871 
Go to UniProtKB:  P25871
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25871
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.14α = 90
b = 63.69β = 107.18
c = 45.61γ = 90
Software Package:
Software NamePurpose
PROCESSdata collection
PROCESSdata reduction
X-PLORmodel building
PROCESSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Other, Refinement description