6SX8 | pdb_00006sx8

Mopeia Virus Exonuclease domain complexed with Manganese

• PDB DOI: https://doi.org/10.2210/pdb6SX8/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Mopeia virus AN20410
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-25 Released: 2021-07-14 
• Deposition Author(s): Nguyen, T.H.V., Ferron, F.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Inhibition of Arenaviridae nucleoprotein exonuclease by bisphosphonate

Nguyen, T.H.V., Yekwa, E., Selisko, B., Canard, B., Alvarez, K., Ferron, F.

(2022) IUCrJ 

• DOI: https://doi.org/10.1107/S2052252522005061

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.37 kDa 
• Atom Count: 3,417 
• Modeled Residue Count: 397 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B	206	Mopeia virus AN20410	Mutation(s): 0  Gene Names: NP EC: 3.1.13
UniProt
Find proteins for Q5S581 (Mopeia virus AN20410) Explore Q5S581  Go to UniProtKB:  Q5S581

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN	D [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.537	α = 90
b = 38.014	β = 92.94
c = 137.23	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Nguyen, T.H.V., Ferron, F.

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Funding Organization	Location	Grant Number
French National Research Agency	France	--

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2022-06-08
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Refinement description