8XEH | pdb_00008xeh

Crystal structure of HEPN-MNT complex

• PDB DOI: https://doi.org/10.2210/pdb8XEH/pdb

• Classification: PROTEIN BINDING
• 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 77.41 kDa 
• Atom Count: 5,252 
• Modeled Residue Count: 623 
• Deposited Residue Count: 664 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MNT	A [auth E]	108	Legionella pneumophila	Mutation(s): 0
UniProt
Find proteins for Q5ZRG1 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZRG1  Go to UniProtKB:  Q5ZRG1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPN	B [auth C], C [auth D], D [auth A], E [auth B]	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.563	α = 90
b = 93.747	β = 123.86
c = 84.958	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.

---

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