8QGR | pdb_00008qgr

Stopper protein of phage 812 in closed conformation

PDB DOI: https://doi.org/10.2210/pdb8QGR/pdb

Classification: VIRUS
Organism(s): Staphylococcus phage 812
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-05 Released: 2024-09-11
Deposition Author(s): Cienikova, Z., Popelarova, B., Plevka, P.
Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.219 (Depositor), 0.227 (DCC)
R-Value Work:
0.190 (Depositor), 0.198 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Genome anchoring, retention, and release by neck proteins of Herelleviridae phage 812

Cienikova, Z., Novacek, J., Siborova, M., Popelarova, B., Fuzik, T., Benesik, M., Bardy, P., Plevka, P.

To be published.

Macromolecule Content

Total Structure Weight: 33.82 kDa
Atom Count: 1,962
Modeled Residue Count: 221
Deposited Residue Count: 292
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	A [auth B]	292	Staphylococcus phage 812	Mutation(s): 0 Gene Names: 812_097, 812_099, 812a_099, 812F1_099, K1/420_099, K1_099
UniProt
Find proteins for A1YTN7 (Staphylococcus phage 812) Explore A1YTN7 Go to UniProtKB: A1YTN7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A1YTN7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.219 (Depositor), 0.227 (DCC)
R-Value Work: 0.190 (Depositor), 0.198 (DCC)

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.366	α = 90
b = 93.366	β = 90
c = 122.531	γ = 120

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: 2024-09-11

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	--

Revision History (Full details and data files)

Version 1.0: 2024-09-11
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.