2VF9

Crystal structure of bacteriophage PRR1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.311 

wwPDB Validation 3D Report Full Report


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

Literature

The Capsid of the Small RNA Phage Prr1 is Stabilized by Metal Ions

Persson, M., Tars, K., Liljas, L.

(2008) J.Mol.Biol. 383: 914

  • DOI: 10.1016/j.jmb.2008.08.060

  • PubMed Abstract: 

    • Many nonenveloped virus particles are stabilized by calcium ions bound in the interfaces between the protein subunits. These ions may have a role in the disassembly process. The small RNA phages of the Leviviridae family have T=3 quasi-symmetry and a ...

    Many nonenveloped virus particles are stabilized by calcium ions bound in the interfaces between the protein subunits. These ions may have a role in the disassembly process. The small RNA phages of the Leviviridae family have T=3 quasi-symmetry and are unique among simple viruses in that they have a coat protein with a translational repressor activity and a fold that has not been observed in other viruses. The crystal structure of phage PRR1 has been determined to 3.5 A resolution. The structure shows a tentative binding site for a calcium ion close to the quasi-3-fold axis. The RNA-binding surface used for repressor activity is mostly conserved. The structure does not show any significant differences between quasi-equivalent subunits, which suggests that the assembly is not controlled by conformational switches as in many other simple viruses.

    Organizational Affiliation: 

    Department of Cell and Molecular Biology, Uppsala University, BMC, Husargatan 3, Box 596, S-751 24 Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAT PROTEIN
A, B, C
131Pseudomonas phage PRR1Mutation(s): 0 
Find proteins for P03616 (Pseudomonas phage PRR1)
Go to UniProtKB:  P03616
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.311 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 281.400α = 93.27
b = 285.400β = 90.00
c = 472.500γ = 119.44
Software Package:
Software NamePurpose
AVEphasing
GLRFphasing
PHASERmodel building
MAMAphasing
MOLEMAN2phasing
PHASERphasing
CNSphasing
DENZOdata reduction
DENZOphasing
CNSmodel building
SCALEPACKphasing
Ophasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2012-02-01
    Type: Other, Version format compliance