Structure of IbpS from Dickeya dadantii

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 

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This is version 1.2 of the entry. See complete history


A secreted metal-binding protein protects necrotrophic phytopathogens from reactive oxygen species.

Liu, L.Gueguen-Chaignon, V.Goncalves, I.R.Rascle, C.Rigault, M.Dellagi, A.Loisel, E.Poussereau, N.Rodrigue, A.Terradot, L.Condemine, G.

(2019) Nat Commun 10: 4853-4853

  • DOI: https://doi.org/10.1038/s41467-019-12826-x
  • Primary Citation of Related Structures:  
    6FJL, 6HHB

  • PubMed Abstract: 

    Few secreted proteins involved in plant infection common to necrotrophic bacteria, fungi and oomycetes have been identified except for plant cell wall-degrading enzymes. Here we study a family of iron-binding proteins that is present in Gram-negative and Gram-positive bacteria, fungi, oomycetes and some animals. Homolog proteins in the phytopathogenic bacterium Dickeya dadantii (IbpS) and the fungal necrotroph Botrytis cinerea (BcIbp) are involved in plant infection. IbpS is secreted, can bind iron and copper, and protects the bacteria against H 2 O 2 -induced death. Its 1.7 Å crystal structure reveals a classical Venus Fly trap fold that forms dimers in solution and in the crystal. We propose that secreted Ibp proteins binds exogenous metals and thus limit intracellular metal accumulation and ROS formation in the microorganisms.

  • Organizational Affiliation

    Microbiologie Adaptation et Pathogénie, UMR 5240 CNRS, Université de Lyon, INSA de Lyon, 69622, Villeurbanne, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-type Fe3+ transport system, periplasmic component
A, B, C, D
345Dickeya dadantii 3937Mutation(s): 0 
Gene Names: Dda3937_02937
Find proteins for E0SCP7 (Dickeya dadantii (strain 3937))
Explore E0SCP7 
Go to UniProtKB:  E0SCP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0SCP7
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.447α = 90
b = 112.313β = 95.53
c = 78.722γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-06
    Type: Initial release
  • Version 1.1: 2020-02-19
    Changes: Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Refinement description