7ZTW | pdb_00007ztw

Crystal Structure of Human Parechovirus 1 2A protein

PDB DOI: https://doi.org/10.2210/pdb7ZTW/pdb

Classification: VIRAL PROTEIN
Organism(s): parechovirus A1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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: 1.93 Å
R-Value Free:
0.238 (Depositor), 0.246 (DCC)
R-Value Work:
0.184 (Depositor), 0.198 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7ZTW

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

Literature

Human Parechovirus 1 2A protein

von Castelmur, E., Perrakis, A.

To be published.

Macromolecule Content

Total Structure Weight: 68.2 kDa
Atom Count: 4,707
Modeled Residue Count: 566
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein 2A	A, B, C, D	150	parechovirus A1	Mutation(s): 1
UniProt
Find proteins for Q66578 (Human parechovirus 1 (strain Harris)) Explore Q66578 Go to UniProtKB: Q66578
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q66578
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain E [auth A]	E [auth A], F [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.238 (Depositor), 0.246 (DCC)
R-Value Work: 0.184 (Depositor), 0.198 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.548	α = 90
b = 127.805	β = 95.19
c = 54.282	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	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: 2023-05-24

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: 2024-06-19
Changes: Data collection

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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.