2X8K | pdb_00002x8k

Crystal Structure of SPP1 Dit (gp 19.1) Protein, a Paradigm of Hub Adsorption Apparatus in Gram-positive Infecting Phages.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.236 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Bacteriophage Spp1 Distal Tail Protein (Gp 19.1): A Baseplate Hub Paradigm in Gram+ Infecting Phages.

Veesler, D.Robin, G.Lichiere, J.Auzat, I.Tavares, P.Bron, P.Campanacci, V.Cambillau, C.

(2010) J Biological Chem 285: 36666

  • DOI: https://doi.org/10.1074/jbc.M110.157529
  • Primary Citation Related Structures: 
    2X8K

  • PubMed Abstract: 

    Siphophage SPP1 infects the gram-positive bacterium Bacillus subtilis using its long non-contractile tail and tail-tip. Electron microscopy (EM) previously allowed a low resolution assignment of most orf products belonging to these regions. We report here the structure of the SPP1 distal tail protein (Dit, gp19.1). The combination of x-ray crystallography, EM, and light scattering established that Dit is a back-to-back dimer of hexamers. However, Dit fitting in the virion EM maps was only possible with a hexamer located between the tail-tube and the tail-tip. Structure comparison revealed high similarity between Dit and a central component of lactophage baseplates. Sequence similarity search expanded its relatedness to several phage proteins, suggesting that Dit is a docking platform for the tail adsorption apparatus in Siphoviridae infecting gram-positive bacteria and that its architecture is a paradigm for these hub proteins. Dit structural similarity extends also to non-contractile and contractile phage tail proteins (gpV(N) and XkdM) as well as to components of the bacterial type 6 secretion system, supporting an evolutionary connection between all these devices.


  • Organizational Affiliation
    • Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS and Universités d'Aix-Marseille I & II, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.

Macromolecule Content 

  • Total Structure Weight: 85.29 kDa 
  • Atom Count: 5,710 
  • Modeled Residue Count: 727 
  • Deposited Residue Count: 756 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HYPOTHETICAL PROTEIN 19.1
A, B, C
252Bacillus phage SPP1Mutation(s): 0 
UniProt
Find proteins for O48459 (Bacillus phage SPP1)
Explore O48459 
Go to UniProtKB:  O48459
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48459
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.236 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.222 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.188α = 90
b = 125.745β = 90
c = 189.353γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other