3LD1 | pdb_00003ld1

Crystal Structure of IBV Nsp2a

• PDB DOI: https://doi.org/10.2210/pdb3LD1/pdb

• Classification: HYDROLASE
• Organism(s): Avian infectious bronchitis virus (strain M41)
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-12 Released: 2011-05-25 
• Deposition Author(s): Xu, Y., Cong, L., Wei, L., Fu, J., Chen, C., Yang, A., Tang, H., Bartlam, M., Rao, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Literature

IBV nsp2 is an endosome-associated protein and viral pathogenicity factor

Xu, Y., Ye, Z., Wei, L., Cong, L., Fu, J., Chen, C., Yang, A., Wu, W., Tang, H., Bartlam, M., Rao, Z.

To be published.

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: 39.76 kDa 
• Atom Count: 2,882 
• Modeled Residue Count: 359 
• Deposited Residue Count: 359 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Replicase polyprotein 1a	A	359	Avian infectious bronchitis virus (strain M41)	Mutation(s): 3  Gene Names: 1a, 1ab EC: 3.4.22
UniProt
Find proteins for P0C6V5 (Avian infectious bronchitis virus (strain M41)) Explore P0C6V5  Go to UniProtKB:  P0C6V5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.179	α = 90
b = 114.179	β = 90
c = 60.979	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-25 
Deposition Author(s): Xu, Y., Cong, L., Wei, L., Fu, J., Chen, C., Yang, A., Tang, H., Bartlam, M., Rao, Z.

Revision History  

• Version 1.0: 2011-05-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references
• Version 1.4: 2024-02-21
  Changes: Data collection