1AUN

PATHOGENESIS-RELATED PROTEIN 5D FROM NICOTIANA TABACUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1006/jmbi.1998.2540

  • 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 crystallogra ...

    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.


    Related Citations: 
    • Purification and Characterization of Tobacco Pathogenesis-Related Protein Pr-5D, an Antifungal Thaumatin-Like Protein
      Koiwa, H.,Kato, H.,Nakatsu, T.,Oda, J.,Yamada, Y.,Sato, F.
      (1997) Plant Cell.Physiol. 38: 783


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PR-5D
A
208Nicotiana tabacumMutation(s): 0 
Gene Names: OLPA (OLP1)
Find proteins for P25871 (Nicotiana tabacum)
Go to UniProtKB:  P25871
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.140α = 90.00
b = 63.690β = 107.18
c = 45.610γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
PROCESSdata collection
PROCESSdata reduction
PROCESSdata scaling
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance