9SIN | pdb_00009sin

Phage epsilon15 tailspike gp20 containing domains beta-helix, beta-sandwich and petal domains with three hexasaccharides of the Salmonella Anatum O-antigen

• PDB DOI: https://doi.org/10.2210/pdb9SIN/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Salmonella phage epsilon15
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-08-28 Released: 2026-09-09 
• Deposition Author(s): Seoane-Blanco, M., van Raaij, M.J.
• Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.167 (DCC) 

Starting Model: experimental

Literature

Structure of the Salmonella bacteriophage epsilon15 tailspike reveals multiple lipopolysaccharide binding sites and protruding esterase domains.

Seoane-Blanco, M., Pereda, A., Broeker, N., McConnell, M., Canada, F.J., Barbirz, S., van Raaij, M.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 96.01 kDa 
• Atom Count: 7,265 
• Modeled Residue Count: 832 
• Deposited Residue Count: 857 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail spike protein	A	857	Salmonella phage epsilon15	Mutation(s): 0  EC: 3.2.1
UniProt
Find proteins for Q858F5 (Salmonella phage epsilon15) Explore Q858F5  Go to UniProtKB:  Q858F5

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
6-O-acetyl-alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-6-O-acetyl-alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose	B	6	N/A	N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose-(1-3)-alpha-D-galactopyranose-(1-6)-beta-D-mannopyranose-(1-4)-alpha-L-rhamnopyranose	C [auth D], D [auth E]	6		N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	T [auth A], U [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.191 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.167 (DCC) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.522	α = 90
b = 117.522	β = 90
c = 250.68	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-09 
Deposition Author(s): Seoane-Blanco, M., van Raaij, M.J.

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Funding Organization	Location	Grant Number
Ministerio de Ciencia e Innovacion (MCIN)	Spain	PID2021-125597NB-I00
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2017-82207-P
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2014-53425-P
Ministerio de Ciencia e Innovacion (MCIN)	Spain	BFU2011-24843/BMC

Revision History  

• Version 1.0: 2026-09-09
  Type: Initial release