4ZPX

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.239
R-Value Work: 0.182
R-Value Observed: 0.184

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6YU74
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.239
R-Value Work: 0.182
R-Value Observed: 0.184
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-05-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-11
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.