7YM5

Crystal structure of the Salmonella effector SseK1

• PDB DOI: https://doi.org/10.2210/pdb7YM5/pdb
• Entry: 7YM5 supersedes: 6AGU

• Classification: TOXIN
• Organism(s): Salmonella enterica
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-07-27 Released: 2023-08-02 
• Deposition Author(s): Kim, U.J., Park, J.B., Yoo, Y., Cho, H.S.
• Funding Organization(s): National Research Foundation (NRF, Korea)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.290 
• R-Value Work: 0.283 
• R-Value Observed: 0.284 

Literature

Crystal structure of the Salmonella effector SseK1

Kim, U.J., Park, J.B., Yoo, Y., Cho, H.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 35.88 kDa 
• Atom Count: 2,493 
• Modelled Residue Count: 304 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III secretion system effector arginine glycosyltransferase SseK1	A	306	Salmonella enterica	Mutation(s): 0  Gene Names: G9F52_004249
UniProt
Find proteins for Q9L9J3 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q9L9J3  Go to UniProtKB:  Q9L9J3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	C [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
MN (Subject of Investigation/LOI)	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 0.290 
• R-Value Work: 0.283 
• R-Value Observed: 0.284 
• Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.995	α = 90
b = 115.995	β = 90
c = 101.042	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
pointless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-02 
Deposition Author(s): Kim, U.J., Park, J.B., Yoo, Y., Cho, H.S.
• This entry supersedes: 6AGU

---

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History  

• Version 1.0: 2023-08-02
  Type: Initial release