8YUF | pdb_00008yuf

Crystal structure of HEPN (Q64A) toxin

• PDB DOI: https://doi.org/10.2210/pdb8YUF/pdb

• Classification: TOXIN
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-03-27 Released: 2025-04-02 
• Deposition Author(s): Jin, C., Jeon, C., Kim, D.H., Lee, B.J.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structural and functional study of HEPN-MNT module from Legionella pneumophila

Jin, C., Jeon, C., Kim, D.H., Lee, B.J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 32.51 kDa 
• Atom Count: 2,505 
• Modeled Residue Count: 267 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyltransferase	A, B	139	Legionella pneumophila	Mutation(s): 1  Gene Names: C3927_14745

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.214 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.774	α = 90
b = 43.772	β = 90
c = 163.302	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Jin, C., Jeon, C., Kim, D.H., Lee, B.J.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1A5A2024425
National Research Foundation (NRF, Korea)	Korea, Republic Of	2021R1F1A1050961

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release