9FXN | pdb_00009fxn

Human mitochondrial nuclease EXOG (hEXOG)

PDB DOI: https://doi.org/10.2210/pdb9FXN/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-07-02 Released: 2024-07-31
Deposition Author(s): Karasinska, J.M., Szymanski, M.R.
Funding Organization(s): European Research Council (ERC), European Molecular Biology Organization (EMBO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.228 (Depositor), 0.230 (DCC)
R-Value Work:
0.157 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Human mitochondrial nuclease EXOG (hEXOG)

Karasinska, J.M., Szymanski, M.R.

(2017) Nat Commun 8: 14959

Macromolecule Content

Total Structure Weight: 72.73 kDa
Atom Count: 5,089
Modeled Residue Count: 601
Deposited Residue Count: 634
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease EXOG, mitochondrial	A, B	317	Homo sapiens	Mutation(s): 0 Gene Names: EXOG, ENDOGL1, ENDOGL2, ENGL EC: 3.1.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2C4 (Homo sapiens) Explore Q9Y2C4 Go to UniProtKB: Q9Y2C4
PHAROS: Q9Y2C4 GTEx: ENSG00000157036
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y2C4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.228 (Depositor), 0.230 (DCC)
R-Value Work: 0.157 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.55	α = 90
b = 83.56	β = 113.51
c = 74.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-31

Deposition Author(s):

Karasinska, J.M.

Szymanski, M.R.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--
European Molecular Biology Organization (EMBO)	European Union	--

Revision History (Full details and data files)

Version 1.0: 2024-07-31
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

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.