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 4EQQ | pdb_00004eqq

Structure of Ltp, a superinfection exclusion protein from the Streptococcus thermophilus temperate phage TP-J34


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.179 (Depositor), 0.177 (DCC) 
  • R-Value Work: 
    0.163 (Depositor) 
  • R-Value Observed: 
    0.164 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4EQQ

This is version 1.3 of the entry. See complete history. 

Literature

X-ray structure of a superinfection exclusion lipoprotein from phage TP-J34 and identification of the tape measure protein as its target.

Bebeacua, C., Lorenzo Fajardo, J.C., Blangy, S., Spinelli, S., Bollmann, S., Neve, H., Cambillau, C., Heller, K.J.

(2013) Mol Microbiol 89: 152-165

  • DOI: https://doi.org/10.1111/mmi.12267
  • Primary Citation Related Structures: 
    4EQQ

  • PubMed Abstract: 

    Lipoproteins of temperate phage are a broad family of membrane proteins encoded in the lysogeny module of temperate phages. Expression of the ltp(TP-J34) gene of temperate Streptococcus thermophilus phage TP-J34 interferes with phage infection at the stage of triggering DNA release and injection into the cell. Here, we report the first structure of a superinfection exclusion protein. We have expressed and determined the X-ray structure of Ltp(TP-J34). The soluble domain of Ltp(TP-J34) is composed of a tandem of three-helix helix-turn-helix (HTH) domains exhibiting a highly negatively charged surface. By isolating mutants of lactococcal phage P008wt with reduced sensitivities to Ltp(TP-J34) and by genome sequencing of such mutants we obtained evidence supporting the notion that Ltp(TP-J34) targets the phage's tape measure protein (TMP) and blocks its insertion into the cytoplasmic membrane.


  • Organizational Affiliation: 
    • Architecture et Fonction des Macromolecules Biologiques, UMR 7257, CNRS and Aix-Marseille University, Case 932, 163 Avenue de Luminy, 13288, Marseille, Cedex 09, France.

Macromolecule Content 

  • Total Structure Weight: 25.28 kDa 
  • Atom Count: 1,986 
  • Modeled Residue Count: 200 
  • Deposited Residue Count: 214 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Putative host cell surface-exposed lipoprotein
A, B
107Streptococcus phage TP-J34Mutation(s): 0 
Gene Names: Ltp
UniProt
Find proteins for O48388 (Streptococcus phage TP-J34)
Explore O48388 
Go to UniProtKB:  O48388
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48388
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
K [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4

Query on PO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
J [auth A]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
N [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.179 (Depositor), 0.177 (DCC) 
  • R-Value Work:  0.163 (Depositor) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.77α = 90
b = 82.77β = 90
c = 100.19γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-03
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations