7TJM | pdb_00007tjm

Bacteriophage Q beta capsid protein in T3 symmetry

• PDB DOI: https://doi.org/10.2210/pdb7TJM/pdb

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Bacteriophage sp.
• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.54 Å
• R-Value Free: 
  0.328 (Depositor), 0.320 (DCC) 
• R-Value Work: 
  0.278 (Depositor), 0.310 (DCC) 
• R-Value Observed: 
  0.281 (Depositor) 

Starting Model: experimental

Literature

Alternative Assembly of Q beta Virus-like Particles

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

To be published.

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: 848.21 kDa 
• Atom Count: 59,580 
• Modeled Residue Count: 7,920 
• Deposited Residue Count: 7,920 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Minor capsid protein A1	A, AA [auth L], AB [auth 4], B [auth a], BA [auth l], BB [auth X], C [auth B], CA [auth M], CB [auth 6], D [auth b], DA [auth m], DB [auth Z], E [auth C], EA [auth N], EB [auth 7], F [auth c], FA [auth n], FB [auth u], G [auth D], GA [auth O], GB [auth 8], H [auth d], HA [auth o], HB [auth 0], I [auth E], IA [auth 9], J [auth e], JA [auth v], K [auth 1], KA [auth P], L [auth U], LA [auth p], M [auth F], MA [auth Q], N [auth f], NA [auth q], O [auth G], OA [auth R], P [auth g], PA [auth r], Q [auth H], QA [auth S], R [auth h], RA [auth s], S [auth I], SA [auth T], T [auth i], TA [auth t], U [auth J], UA [auth w], V [auth j], VA [auth x], W [auth 5], WA [auth 2], X [auth Y], XA [auth V], Y [auth K], YA [auth 3], Z [auth k], ZA [auth W]	132	Bacteriophage sp.	Mutation(s): 0
UniProt
Find proteins for Q8LTE1 (Escherichia virus Qbeta) Explore Q8LTE1  Go to UniProtKB:  Q8LTE1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.54 Å
• R-Value Free:  0.328 (Depositor), 0.320 (DCC) 
• R-Value Work:  0.278 (Depositor), 0.310 (DCC) 
• R-Value Observed: 0.281 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 286.627	α = 90
b = 286.627	β = 90
c = 662.678	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Jin, X.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-09
  Changes: Structure summary