8X4K | pdb_00008x4k

Crystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPDGlc

• PDB DOI: https://doi.org/10.2210/pdb8X4K/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: 1.90 Å
• R-Value Free: 
  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the glycosyltransferase domain of Legionella SetA in complex with UPDGlc

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: 53.29 kDa 
• Atom Count: 3,882 
• Modeled Residue Count: 452 
• Deposited Residue Count: 458 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Subversion of eukaryotic traffic protein A	A	458	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UDP (Subject of Investigation/LOI)	B [auth A]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
BGC (Subject of Investigation/LOI)	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.211 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.14	α = 90
b = 63.257	β = 90
c = 184.962	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	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