7ZUA | pdb_00007zua

Crystal Structure of Ljungan virus 4 2A2 protein I222 crystal form

PDB DOI: https://doi.org/10.2210/pdb7ZUA/pdb

Classification: VIRAL PROTEIN
Organism(s): Ljungan virus 64-7855
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-05-11 Released: 2023-05-24
Deposition Author(s): von Castelmur, E., Perrakis, A.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.256 (Depositor), 0.270 (DCC)
R-Value Work:
0.209 (Depositor), 0.220 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Structural plasticity of Parechovirus family H-box 2A proteins

von Castelmur, E., Perrakis, A.

To be published.

Macromolecule Content

Total Structure Weight: 13.8 kDa
Atom Count: 980
Modeled Residue Count: 118
Deposited Residue Count: 125
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein 2A	A	125	Ljungan virus 64-7855	Mutation(s): 0
UniProt
Find proteins for C0J6D4 (Ljungan virus 64-7855) Explore C0J6D4 Go to UniProtKB: C0J6D4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C0J6D4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.256 (Depositor), 0.270 (DCC)
R-Value Work: 0.209 (Depositor), 0.220 (DCC)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.513	α = 90
b = 59.562	β = 90
c = 72.827	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-05-24

Deposition Author(s):

von Castelmur, E.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2023-05-24
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary

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.