3RLK | pdb_00003rlk

Crystal structure of the read-through domain from bacteriophage Qbeta A1 protein, monoclinic crystal form

• PDB DOI: https://doi.org/10.2210/pdb3RLK/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Qubevirus durum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-04-19 Released: 2011-09-28 
• Deposition Author(s): Rumnieks, J., Tars, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of the read-through domain from bacteriophage Qbeta A1 protein

Rumnieks, J., Tars, K.

(2011) Protein Sci 20: 1707-1712

• PubMed: 21805520 
• DOI: https://doi.org/10.1002/pro.704
• Primary Citation Related Structures: 
  3RLC, 3RLK


• PubMed Abstract: 
  

  Bacteriophage Qβ is a small RNA virus that infects Escherichia coli. The virus particle contains a few copies of the minor coat protein A1, a C-terminally prolonged version of the coat protein, which is formed when ribosomes occasionally read-through the leaky stop codon of the coat protein. The crystal structure of the read-through domain from bacteriophage Qβ A1 protein was determined at a resolution of 1.8 Å. The domain consists of a heavily deformed five-stranded β-barrel on one side of the protein and a β-hairpin and a three-stranded β-sheet on the other. Several short helices and well-ordered loops are also present throughout the protein. The N-terminal part of the read-through domain contains a prominent polyproline type II helix. The overall fold of the domain is not similar to any published structure in the Protein Data Bank.

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Organizational Affiliation: 
• Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga LV-1067, Latvia. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.99 kDa 
• Atom Count: 1,631 
• Modeled Residue Count: 183 
• Deposited Residue Count: 192 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
A1 protein	A	192	Qubevirus durum	Mutation(s): 0  Gene Names: A1
UniProt
Find proteins for Q8LTE1 (Escherichia virus Qbeta) Explore Q8LTE1  Go to UniProtKB:  Q8LTE1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.242 (Depositor), 0.242 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.01	α = 90
b = 49.12	β = 118.41
c = 44.26	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-28 
Deposition Author(s): Rumnieks, J., Tars, K.

Revision History  

• Version 1.0: 2011-09-28
  Type: Initial release
  
• Version 1.1: 2013-06-26
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations