7TJD | pdb_00007tjd

Bacteriophage Q beta capsid protein in T1 symmetry

PDB DOI: https://doi.org/10.2210/pdb7TJD/pdb

Classification: VIRUS LIKE PARTICLE
Organism(s): Qubevirus durum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-16 Released: 2023-01-25
Deposition Author(s): Jin, X.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Alternative Assembly of Q beta Virus-like Particles

Shaw, V., Sungsuwan, S., McFall-Boegeman, H., Huang, X., Jin, X.

To be published.

Macromolecule Content

Total Structure Weight: 282.74 kDa
Atom Count: 19,860
Modeled Residue Count: 2,640
Deposited Residue Count: 2,640
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein A1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	132	Qubevirus durum	Mutation(s): 0
UniProt
Find proteins for Q8LTE1 (Escherichia virus Qbeta) Explore Q8LTE1 Go to UniProtKB: Q8LTE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8LTE1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.50 Å
R-Value Free: 0.250 (Depositor), 0.250 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 271.926	α = 90
b = 271.926	β = 90
c = 166.564	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		--

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-10-25
Changes: Data collection, Refinement description
Version 1.2: 2024-11-13
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.