9EQP

N-terminal domain of Infectious Bursal Disease Virus (IBDV) VP3

PDB DOI: https://doi.org/10.2210/pdb9EQP/pdb

Classification: VIRAL PROTEIN
Organism(s): Infectious bursal disease virus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2024-03-22 Released: 2024-10-09
Deposition Author(s): Ferrero, D.S., Verdaguer, N.
Funding Organization(s): Spanish Ministry of Science, Innovation, and Universities

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.259
R-Value Work: 0.238
R-Value Observed: 0.239

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of the amino terminal domain of the Birnaviral multifunctional VP3 protein and its unexplored critical role.

Ferrero, D.S., Verdaguer, N.

To be published.

Macromolecule Content

Total Structure Weight: 120.14 kDa
Atom Count: 8,353
Modelled Residue Count: 1,040
Deposited Residue Count: 1,048
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP3	A B C D E A, B, C, D, E, F, G, H [auth I]	131	Infectious bursal disease virus	Mutation(s): 0
UniProt
Find proteins for P61825 (Avian infectious bursal disease virus) Explore P61825 Go to UniProtKB: P61825
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61825
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.259
R-Value Work: 0.238
R-Value Observed: 0.239
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.687	α = 90
b = 111.416	β = 90
c = 277.012	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Spanish Ministry of Science, Innovation, and Universities	Spain	PID2020-117976GB-I00

Revision History (Full details and data files)

Version 1.0: 2024-10-09
Type: Initial release

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.