4ZPX | pdb_00004zpx

Crystal structure of Lon ATPase domain from Thermococcus onnurineus NA1

• PDB DOI: https://doi.org/10.2210/pdb4ZPX/pdb

• Classification: HYDROLASE
• Organism(s): Thermococcus onnurineus NA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-05-08 Released: 2016-05-11 
• Deposition Author(s): An, Y.J., Kim, M.I., Na, J.H., Cha, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Structural disparity classifies AAA+ modules of Lon proteases into two distinct clades

Kim, M.I., An, Y.J., Na, J.H., Cha, S.S.

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.

Macromolecule Content 

• Total Structure Weight: 92.05 kDa 
• Atom Count: 5,207 
• Modeled Residue Count: 658 
• Deposited Residue Count: 826 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent protease Lon	A, B	413	Thermococcus onnurineus NA1	Mutation(s): 0  Gene Names: TON_0529
UniProt
Find proteins for B6YU74 (Thermococcus onnurineus (strain NA1)) Explore B6YU74  Go to UniProtKB:  B6YU74

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.03 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.62	α = 74.61
b = 61.599	β = 87.11
c = 76.321	γ = 83.45

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-11 
Deposition Author(s): An, Y.J., Kim, M.I., Na, J.H., Cha, S.S.

Revision History  

• Version 1.0: 2016-05-11
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection, Database references, Derived calculations
• Version 1.2: 2024-10-23
  Changes: Data collection, Database references, Structure summary