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), 0.268 (DCC)
R-Value Work:
0.209 (Depositor), 0.219 (DCC)

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

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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.268 (DCC)
R-Value Work: 0.209 (Depositor), 0.219 (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

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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

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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.