4A1N | pdb_00004a1n

Human Mitochondrial endo-exonuclease

• PDB DOI: https://doi.org/10.2210/pdb4A1N/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-16 Released: 2012-02-29 
• Deposition Author(s): Welin, M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Nyman, T., Persson, C., Schuler, H., Thorsell, A.G., Tresaugues, L., Weigelt, J., Nordlund, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.225 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.175 (Depositor) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Human Mitochondrial Endo-Exonuclease

Welin, M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Nyman, T., Persson, C., Schuler, H., Thorsell, A.G., Tresaugues, L., Weigelt, J., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.1 kDa 
• Atom Count: 2,379 
• Modeled Residue Count: 290 
• Deposited Residue Count: 335 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NUCLEASE EXOG, MITOCHONDRIAL	A	335	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.225 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.175 (Depositor) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.18	α = 90
b = 103.18	β = 90
c = 83.89	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Welin, M., Moche, M., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Graslund, S., Hammarstrom, M., Johansson, I., Karlberg, T., Kotenyova, T., Nyman, T., Persson, C., Schuler, H., Thorsell, A.G., Tresaugues, L., Weigelt, J., Nordlund, P.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description