2POS

Crystal Structure of sylvaticin, a new secreted protein from pythium sylvaticum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of sylvaticin, a new alpha-elicitin-like protein from Pythium sylvaticum.

Lascombe, M.B.Retailleau, P.Ponchet, M.Industri, B.Blein, J.P.Prange, T.

(2007) Acta Crystallogr.,Sect.D 63: 1102-1108

  • DOI: 10.1107/S0907444907043363
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of sylvaticin, a 10 kDa major pythin protein excreted by the parasitic oomycete Pythium sylvaticum, has been determined. Although closely related to alpha-elicitins in its biological response, toxicity and overall structure, sylvaticin ...

    The structure of sylvaticin, a 10 kDa major pythin protein excreted by the parasitic oomycete Pythium sylvaticum, has been determined. Although closely related to alpha-elicitins in its biological response, toxicity and overall structure, sylvaticin presents a number of structural features that make it an unusual member of the elicitin class. Elicitins possess a large hydrophobic cavity and the mechanism of the systemic acquired resistance induced in planta is known to proceed through lipid transport and complexation within this cavity. Unlike other elicitins, sylvaticin contains tryptophan residues, one of which points inwards towards the central cavity, thus limiting access to sterols. In the case of sylvaticin, the sterol-transport mechanism is likely to be of less importance compared with other members of the elicitin family and still remains to be fully characterized.


    Related Citations: 
    • Purification,crystallisation and preliminary X-ray studies of sylvaticin, an elicitin-like protein from pythium sylvaticum
      Lascombe, M.B.,Ponchet, M.,Cardin, L.,Milat, M.L.,Blein, J.P.,Prange, T.
      (2004) Acta Crystallogr.,Sect.D D60: 362


    Organizational Affiliation

    Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, UMR 8015 CNRS, Faculté de Pharmacie, 4 Avenue de l'Observatoire, 75006 Paris, France. marie-bernard.lascombe@univ-paris5.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SYLVATICIN
A, B, C, D
94Pythium sylvaticumMutation(s): 0 
Find proteins for D0VWX7 (Pythium sylvaticum)
Go to UniProtKB:  D0VWX7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B, C, D
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.220α = 85.20
b = 46.000β = 71.27
c = 55.730γ = 74.63
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
ADSCdata collection
XDSdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance