7QRR | pdb_00007qrr

Crystal structure of Noumeavirus NMV_189 protein

PDB DOI: https://doi.org/10.2210/pdb7QRR/pdb

Classification: VIRAL PROTEIN
Organism(s): Noumeavirus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-11 Released: 2023-01-25
Deposition Author(s): Jeudy, S., Abergel, C.
Funding Organization(s): Agence Nationale de la Recherche (ANR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.191 (Depositor), 0.190 (DCC)
R-Value Work:
0.162 (Depositor), 0.160 (DCC)
R-Value Observed:
0.163 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The fibre head structure used by unrelated families of viruses is unexpectedly a major component of the Marseilleviridae and Zamilon virophages capsids

Jeudy, S., Abergel, C.

To be published.

Macromolecule Content

Total Structure Weight: 191.28 kDa
Atom Count: 14,991
Modeled Residue Count: 1,764
Deposited Residue Count: 1,836
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NMV_189 protein	A [auth F] B [auth A] C [auth B] D [auth C] E [auth D] A [auth F], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G, H, I, J, K, L	153	Noumeavirus	Mutation(s): 0 Gene Names: NMV_189
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain N [auth E] MOL2 format, chain N [auth E] mmCIF format, chain N [auth E]	N [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth E] Interactions & Density Focus chain N [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth F] MOL2 format, chain M [auth F] mmCIF format, chain M [auth F]	M [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth F] Interactions & Density Focus chain M [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.191 (Depositor), 0.190 (DCC)
R-Value Work: 0.162 (Depositor), 0.160 (DCC)
R-Value Observed: 0.163 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 221.567	α = 90
b = 111.852	β = 122.62
c = 127.897	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Agence Nationale de la Recherche (ANR)	France	ANR-20-CE11-0001

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2024-06-19
Changes: Data collection

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.