8XDJ

Crystal structure of AMPylated HEPN toxin

• PDB DOI: https://doi.org/10.2210/pdb8XDJ/pdb

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


• Deposited: 2023-12-11 Released: 2024-12-18 
• 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: 1.65 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

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 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 66.63 kDa 
• Atom Count: 4,811 
• Modelled Residue Count: 526 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPN toxin	A, B, C, D	139	Legionella pneumophila	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP (Subject of Investigation/LOI)	E [auth A], G [auth B], H [auth C], J [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	F [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.204 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.199	α = 90
b = 53.296	β = 122.31
c = 88.021	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-18 
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: 2024-12-18
  Type: Initial release