1GAV | pdb_00001gav

BACTERIOPHAGE GA PROTEIN CAPSID

• PDB DOI: https://doi.org/10.2210/pdb1GAV/pdb

• Classification: VIRUS
• Organism(s): Enterobacteria phage GA
• Mutation(s): Yes 


• Deposited: 1997-01-28 Released: 1997-09-04 
• Deposition Author(s): Tars, K., Bundule, M., Liljas, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Work: 
  0.279 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.279 (Depositor) 

Literature

The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses.

Tars, K., Bundule, M., Fridborg, K., Liljas, L.

(1997) J Mol Biology 271: 759-773

• PubMed: 9299325 
• DOI: https://doi.org/10.1006/jmbi.1997.1214
• Primary Citation Related Structures: 
  1GAV


• PubMed Abstract: 
  

  The three-dimensional structure of the small T=3 RNA bacteriophage GA has been determined at 3.4 A resolution. The structure was solved by molecular replacement, using the phage MS2 as an initial model. A comparison of the protein shells of the four related phages GA, MS2, fr and Qbeta was carried out in order to define structural features of particular importance for their assembly and specific RNA interaction. A high degree of similarity was found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat proteins, especially in the FG loops forming 5-fold and quasi-6-fold contacts. The overall arrangement of the protein subunits in the shells of these phages is very similar, although the details of the interactions differ. The few conserved interactions are suggested to govern the subunit packing during assembly.

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Organizational Affiliation: 
• Biomedical Research and Study Centre, Latvian University, Ratsupites 1, Riga, Latvia.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 180-mer - A180 

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

Macromolecule Content 

• Total Structure Weight: 613.59 kDa 
• Atom Count: 43,335 
• Modeled Residue Count: 5,805 
• Deposited Residue Count: 5,805 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BACTERIOPHAGE GA PROTEIN CAPSID	A, AA [auth 1], B, BA [auth 2], C, CA [auth 3], D, DA [auth 4], E, EA [auth 5], F, FA [auth 6], G, GA [auth 7], H, HA [auth 8], I, IA [auth 9], J, JA [auth 0], K, KA [auth a], L, LA [auth b], M, MA [auth c], N, NA [auth d], O, OA [auth e], P, PA [auth f], Q, QA [auth g], R, RA [auth h], S, SA [auth i], T, U, V, W, X, Y, Z	129	Enterobacteria phage GA	Mutation(s): 2
UniProt
Find proteins for P07234 (Enterobacteria phage GA) Explore P07234  Go to UniProtKB:  P07234

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Work:  0.279 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.279 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 272.7	α = 90
b = 293.5	β = 90
c = 339.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-04 
Deposition Author(s): Tars, K., Bundule, M., Liljas, L.

Revision History  

• Version 1.0: 1997-09-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Other