2PR0 | pdb_00002pr0

Crystal structure of Sylvaticin, a new secreted protein from Pythium Sylvaticum

• PDB DOI: https://doi.org/10.2210/pdb2PR0/pdb

• Classification: TOXIN
• Organism(s): Globisporangium sylvaticum
• Mutation(s): No 


• Deposited: 2007-05-03 Released: 2008-03-18 
• Deposition Author(s): Lascombe, M.B., Prange, T., Retailleau, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 
  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

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

• PubMed: 17881828 
• DOI: https://doi.org/10.1107/S0907444907043363
• Primary Citation 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 21.18 kDa 
• Atom Count: 1,683 
• Modeled Residue Count: 188 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
sylvaticin	A, B	94	Globisporangium sylvaticum	Mutation(s): 0
UniProt
Find proteins for D0VWX7 (Globisporangium sylvaticum) Explore D0VWX7  Go to UniProtKB:  D0VWX7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A], F [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
NI	C [auth A], E [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free:  0.186 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.692	α = 90
b = 25.974	β = 99.69
c = 68.349	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): Lascombe, M.B., Prange, T., Retailleau, P.

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary