6OV6

CRYSTALLOGRAPHIC STRUCTURE OF THE C24 PROTEIN FROM THE ANTARCTIC MICROORGANISM BIZIONIA ARGENTINENSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the putative long tail fiber receptor-binding tip of a novel temperate bacteriophage from the Antarctic bacterium Bizionia argentinensis JUB59.

Pellizza, L.Lopez, J.L.Vazquez, S.Sycz, G.Guimaraes, B.G.Rinaldi, J.Goldbaum, F.A.Aran, M.Mac Cormack, W.P.Klinke, S.

(2020) J Struct Biol 212: 107595-107595

  • DOI: https://doi.org/10.1016/j.jsb.2020.107595
  • Primary Citation of Related Structures:  
    6OV6

  • PubMed Abstract: 

    Tailed bacteriophages are one of the most widespread biological entities on Earth. Their singular structures, such as spikes or fibers are of special interest given their potential use in a wide range of biotechnological applications. In particular, the long fibers present at the termini of the T4 phage tail have been studied in detail and are important for host recognition and adsorption. Although significant progress has been made in elucidating structural mechanisms of model phages, the high-resolution structural description of the vast population of marine phages is still unexplored. In this context, we present here the crystal structure of C24, a putative receptor-binding tip-like protein from Bizionia argentinensis JUB59, a psychrotolerant bacterium isolated from the marine surface waters of Potter Cove, Antarctica. The structure resembles the receptor-binding tip from the bacteriophage T4 long tail fiber yet showing marked differences in its domain organization, size, sequence identity and metal binding nature. We confirmed the viral origin of C24 by induction experiments using mitomycin C. Our results reveal the presence of a novel uncharacterized prophage in the genome of B. argentinensis JUB59, whose morphology is compatible with the order Caudovirales and that carries the nucleotide sequence of C24 in its genome. This work provides valuable information to expand our current knowledge on the viral machinery prevalent in the oceans.


  • Organizational Affiliation

    Fundación Instituto Leloir, IIBBA-CONICET, Patricias Argentinas 435 (C1405BWE), Buenos Aires, Argentina.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C24 PROTEIN
A, B, C
277Bizionia argentinensis JUB59Mutation(s): 0 
Gene Names: BZARG_797
UniProt
Find proteins for G2EBB4 (Bizionia argentinensis JUB59)
Explore G2EBB4 
Go to UniProtKB:  G2EBB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2EBB4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.13α = 90
b = 65.25β = 90
c = 239.53γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
SHELXphasing
BUSTERrefinement
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-10-07
    Changes: Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references