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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.239 (Depositor), 0.238 (DCC)
R-Value Work:
0.182 (Depositor), 0.189 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4ZPX

This is version 1.2 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
Modeled Residue Count: 658
Deposited Residue Count: 826
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF 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 (Depositor), 0.238 (DCC)
R-Value Work: 0.182 (Depositor), 0.189 (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

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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
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.