2POS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 D Biol Crystallogr 63: 1102-1108

  • DOI: https://doi.org/10.1107/S0907444907043363
  • Primary Citation of Related Structures:  
    2POS, 2PR0

  • 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 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.


  • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SYLVATICIN
A, B, C, D
94Globisporangium sylvaticumMutation(s): 0 
UniProt
Find proteins for D0VWX7 (Globisporangium sylvaticum)
Explore D0VWX7 
Go to UniProtKB:  D0VWX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
NI
Query on NI

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.152 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.22α = 85.2
b = 46β = 71.27
c = 55.73γ = 74.63
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description