8XEM | pdb_00008xem

Crystal structure of apo HEPN toxin

• PDB DOI: https://doi.org/10.2210/pdb8XEM/pdb

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


• Deposited: 2023-12-12 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: 1.80 Å
• R-Value Free: 
  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: in silico

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.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.25 kDa 
• Atom Count: 4,775 
• Modeled Residue Count: 525 
• Deposited Residue Count: 556 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPN	A, B, C, D	139	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for Q5ZRG2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRG2  Go to UniProtKB:  Q5ZRG2

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.208 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.88	α = 90
b = 53.185	β = 122.1
c = 86.965	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