8X4J | pdb_00008x4j

Crystal structure of the glycosyltransferase domain of Legionella SetA (unbound)

• PDB DOI: https://doi.org/10.2210/pdb8X4J/pdb

• Classification: TRANSFERASE
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-11-15 Released: 2025-02-19 
• Deposition Author(s): Im, H.N., Lee, Y., Jang, D.M., Hahn, H., Kim, H.S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 
  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Legionella effector SetA glycosyltransferase domain in the unbound form

Im, H.N., Lee, Y., Jang, D.M., Hahn, H., Kim, 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 (software)

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 53.81 kDa 
• Atom Count: 3,663 
• Modeled Residue Count: 446 
• Deposited Residue Count: 469 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subversion of eukaryotic traffic protein A	A	469	Legionella pneumophila	Mutation(s): 0  Gene Names: setA EC: 2.4.1
UniProt
Find proteins for Q5ZU30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZU30  Go to UniProtKB:  Q5ZU30

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free:  0.247 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.413	α = 90
b = 139.413	β = 90
c = 59.944	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-02-19 
Deposition Author(s): Im, H.N., Lee, Y., Jang, D.M., Hahn, H., Kim, H.S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-02-19
  Type: Initial release