5XBC | pdb_00005xbc

Crystal Structure Basis for PEDV nsp1

• PDB DOI: https://doi.org/10.2210/pdb5XBC/pdb

• Classification: HYDROLASE
• Organism(s): Porcine epidemic diarrhea virus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2017-03-16 Released: 2017-12-13 
• Deposition Author(s): Shen, Z., Peng, G.Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal Structure Basis for PEDV nsp1

Shen, Z., Peng, G.Q.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.23 kDa 
• Atom Count: 2,184 
• Modeled Residue Count: 235 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
nsp1 protein	A, B	118	Porcine epidemic diarrhea virus	Mutation(s): 0
UniProt
Find proteins for K4L9I6 (Porcine epidemic diarrhea virus) Explore K4L9I6  Go to UniProtKB:  K4L9I6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.193 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.709	α = 90
b = 75.053	β = 89.96
c = 37.363	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-13 
Deposition Author(s): Shen, Z., Peng, G.Q.

Revision History  

• Version 1.0: 2017-12-13
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references