8A2G | pdb_00008a2g

Crystal structure of Sebokelevirus 2A2 protein

PDB DOI: https://doi.org/10.2210/pdb8A2G/pdb

Classification: VIRAL PROTEIN
Organism(s): parechovirus C1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-06-03 Released: 2023-06-14
Deposition Author(s): Zhu, L., Von Castelmur, E., Whang, X., Ren, J., Fry, E., Perrakis, A., Stuart, D.I.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.202 (Depositor), 0.210 (DCC)
R-Value Work:
0.170 (Depositor), 0.182 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8A2G

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

Literature

Structural plasticity of 2A proteins in the Parechovirus family

Von Castelmur, E., Zhu, L., Perrakis, A.

To be published.

Macromolecule Content

Total Structure Weight: 32.05 kDa
Atom Count: 2,565
Modeled Residue Count: 290
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2A2 protein	A, B	146	parechovirus C1	Mutation(s): 0
UniProt
Find proteins for S0DHJ0 (parechovirus C1) Explore S0DHJ0 Go to UniProtKB: S0DHJ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	S0DHJ0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.202 (Depositor), 0.210 (DCC)
R-Value Work: 0.170 (Depositor), 0.182 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.35	α = 90
b = 69.73	β = 90
c = 57.27	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-14

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: 2023-06-14
Type: Initial release
Version 1.1: 2024-02-07
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.