3UXF | pdb_00003uxf

Structure of the fimbrial protein FimP from Actonomyces oris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.196 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The Pilin Protein FimP from Actinomyces oris: Crystal Structure and Sequence Analyses.

Persson, K.Esberg, A.Claesson, R.Stromberg, N.

(2012) PLoS One 7: e48364-e48364

  • DOI: https://doi.org/10.1371/journal.pone.0048364
  • Primary Citation Related Structures: 
    3UXF

  • PubMed Abstract: 

    The Actinomyces oris type-1 pili are important for the initial formation of dental plaque by binding to salivary proteins that adhere to the tooth surface. Here we present the X-ray structure of FimP, the protein that is polymerized into the type-1 pilus stalk, assisted by a pili-specific sortase. FimP consists of three tandem IgG-like domains. The middle and C-terminal domains contain one autocatalyzed intramolecular isopeptide bond each, a feature used by Gram-positive bacteria for stabilization of surface proteins. While the N-terminal domain harbours all the residues necessary for forming an isopeptide bond, no such bond is observed in the crystal structure of this unpolymerized form of FimP. The monomer is further stabilized by one disulfide bond each in the N- and C-terminal domains as well as by a metal-coordinated loop protruding from the C-terminal domain. A lysine, predicted to be crucial for FimP polymerization by covalent attachment to a threonine from another subunit, is located at the rim of a groove lined with conserved residues. The groove may function as a docking site for the sortase-FimP complex. We also present sequence analyses performed on the genes encoding FimP as well as the related FimA, obtained from clinical isolates.


  • Organizational Affiliation
    • Department of Chemistry, Umeå University, Umeå, Sweden. karina.persson@chem.umu.se

Macromolecule Content 

  • Total Structure Weight: 53.29 kDa 
  • Atom Count: 4,267 
  • Modeled Residue Count: 449 
  • Deposited Residue Count: 488 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fimbrial subunit type 1488Actinomyces orisMutation(s): 1 
Gene Names: FimP
UniProt
Find proteins for P18477 (Actinomyces viscosus)
Explore P18477 
Go to UniProtKB:  P18477
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18477
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.196 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.239α = 90
b = 176.587β = 90
c = 40.119γ = 90
Software Package:
Software NamePurpose
EDNAdata collection
Auto-Rickshawphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2012-11-28 
  • Deposition Author(s): Persson, K.

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-28
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Structure summary
  • Version 1.2: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary