6SY8 | pdb_00006sy8

Mopeia Virus Exonuclease domain fully depleted of Manganese un ALD compound

PDB DOI: https://doi.org/10.2210/pdb6SY8/pdb

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

Deposited: 2019-09-27 Released: 2021-07-14
Deposition Author(s): Nguyen, T.H.V., Ferron, F.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.283 (Depositor), 0.282 (DCC)
R-Value Work:
0.248 (Depositor), 0.256 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 47.26 kDa
Atom Count: 3,302
Modeled Residue Count: 397
Deposited Residue Count: 412
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoprotein	A, B	206	Mopeia virus AN20410	Mutation(s): 0 Gene Names: NP, N EC: 3.1.13
UniProt
Find proteins for Q5S581 (Mopeia virus AN20410) Explore Q5S581 Go to UniProtKB: Q5S581
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5S581
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.08 Å
R-Value Free: 0.283 (Depositor), 0.282 (DCC)
R-Value Work: 0.248 (Depositor), 0.256 (DCC)
R-Value Observed: 0.250 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.853	α = 90
b = 38.29	β = 92.63
c = 137.315	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.