Crystal Structure of the Pseudomonas phage phi297 tailspike gp61

Experimental Data Snapshot

  • Resolution: 1.52 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.079 
  • R-Value Observed: 0.081 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The O-specific polysaccharide lyase from the phage LKA1 tailspike reduces Pseudomonas virulence.

Olszak, T.Shneider, M.M.Latka, A.Maciejewska, B.Browning, C.Sycheva, L.V.Cornelissen, A.Danis-Wlodarczyk, K.Senchenkova, S.N.Shashkov, A.S.Gula, G.Arabski, M.Wasik, S.Miroshnikov, K.A.Lavigne, R.Leiman, P.G.Knirel, Y.A.Drulis-Kawa, Z.

(2017) Sci Rep 7: 16302-16302

  • DOI: https://doi.org/10.1038/s41598-017-16411-4
  • Primary Citation of Related Structures:  
    4RU4, 4RU5

  • PubMed Abstract: 

    Pseudomonas phage LKA1 of the subfamily Autographivirinae encodes a tailspike protein (LKA1gp49) which binds and cleaves B-band LPS (O-specific antigen, OSA) of Pseudomonas aeruginosa PAO1. The crystal structure of LKA1gp49 catalytic domain consists of a beta-helix, an insertion domain and a C-terminal discoidin-like domain. The putative substrate binding and processing site is located on the face of the beta-helix whereas the C-terminal domain is likely involved in carbohydrates binding. NMR spectroscopy and mass spectrometry analyses of degraded LPS (OSA) fragments show an O5 serotype-specific polysaccharide lyase specificity. LKA1gp49 reduces virulence in an in vivo Galleria mellonella infection model and sensitizes P. aeruginosa to serum complement activity. This enzyme causes biofilm degradation and does not affect the activity of ciprofloxacin and gentamicin. This is the first comprehensive report on LPS-degrading lyase derived from a Pseudomonas phage. Biological properties reveal a potential towards its applications in antimicrobial design and as a microbiological or biotechnological tool.

  • Organizational Affiliation

    Institute of Genetics and Microbiology, University of Wroclaw, Wroclaw, 51-148, Poland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tailspike gp27
A, B, C
605Pseudomonas phage phi297Mutation(s): 0 
Gene Names: phi297_00061
Find proteins for H2BD96 (Pseudomonas phage phi297)
Explore H2BD96 
Go to UniProtKB:  H2BD96
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH2BD96
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EDO

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
GA [auth C]
HA [auth C]
IA [auth C]
EA [auth C],
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
JA [auth C],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
U [auth B],
V [auth B],
W [auth B]
C2 H6 O2
Query on ACT

Download Ideal Coordinates CCD File 
KA [auth C]
LA [auth C]
MA [auth C]
P [auth A]
X [auth B]
KA [auth C],
LA [auth C],
MA [auth C],
P [auth A],
X [auth B],
Y [auth B],
Z [auth B]
C2 H3 O2
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
D [auth A]
E [auth A]
Q [auth B]
AA [auth C],
BA [auth C],
D [auth A],
E [auth A],
Q [auth B],
R [auth B]
Query on NA

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
F [auth A]
G [auth A]
H [auth A]
CA [auth C],
DA [auth C],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
S [auth B],
T [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.52 Å
  • R-Value Free: 0.120 
  • R-Value Work: 0.079 
  • R-Value Observed: 0.081 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 210.617α = 90
b = 124.705β = 97.93
c = 83.563γ = 90
Software Package:
Software NamePurpose
RemDAqdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Refinement description
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2018-04-18
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary