2QJ1 | pdb_00002qj1

Crystal structure of infectious bursal disease virus VP1 polymerase incubated with an oligopeptide mimicking the VP3 C-terminus

• PDB DOI: https://doi.org/10.2210/pdb2QJ1/pdb

• Classification: TRANSFERASE
• Organism(s): Infectious bursal disease virus
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2007-07-06 Released: 2007-11-27 
• Deposition Author(s): Garriga, D., Navarro, A., Querol-Audi, J., Abaitua, F., Rodriguez, J.F., Verdaguer, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.48 Å
• R-Value Free: 
  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.241 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Unprecedented activation mechanism of a non-canonical RNA-dependent RNA polymerase

Garriga, D., Navarro, A., Querol-Audi, J., Abaitua, F., Rodriguez, J.F., Verdaguer, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.65 kDa 
• Atom Count: 5,927 
• Modeled Residue Count: 767 
• Deposited Residue Count: 852 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Infectious bursal disease virus VP1 polymerase	A	852	Infectious bursal disease virus	Mutation(s): 0  Gene Names: VP1 EC: 2.7.7.48
UniProt
Find proteins for Q9Q6Q5 (Avian infectious bursal disease virus) Explore Q9Q6Q5  Go to UniProtKB:  Q9Q6Q5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.48 Å
• R-Value Free:  0.281 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.241 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.913	α = 90
b = 121.913	β = 90
c = 359.426	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-27 
Deposition Author(s): Garriga, D., Navarro, A., Querol-Audi, J., Abaitua, F., Rodriguez, J.F., Verdaguer, N.

Revision History  

• Version 1.0: 2007-11-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Advisory, Refinement description
• Version 1.3: 2023-08-30
  Changes: Advisory, Data collection, Database references, Refinement description