4R8T

Structure of JEV protease

• PDB DOI: https://doi.org/10.2210/pdb4R8T/pdb

• Classification: HYDROLASE
• Organism(s): Japanese encephalitis virus strain Nakayama, Japanese encephalitis virus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-09-03 Released: 2014-12-24 
• Deposition Author(s): Nair, D.T., Weinert, T., Wang, M., Olieric, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.218 
• R-Value Work: 0.164 
• R-Value Observed: 0.170 

Literature

Fast native-SAD phasing for routine macromolecular structure determination.

Weinert, T., Olieric, V., Waltersperger, S., Panepucci, E., Chen, L., Zhang, H., Zhou, D., Rose, J., Ebihara, A., Kuramitsu, S., Li, D., Howe, N., Schnapp, G., Pautsch, A., Bargsten, K., Prota, A.E., Surana, P., Kottur, J., Nair, D.T., Basilico, F., Cecatiello, V., Pasqualato, S., Boland, A., Weichenrieder, O., Wang, B.C., Steinmetz, M.O., Caffrey, M., Wang, M.

(2015) Nat Methods 12: 131-133

• PubMed: 25506719 
• DOI: https://doi.org/10.1038/nmeth.3211
• Primary Citation of Related Structures:  
  4PGO, 4PII, 4R8T, 4R8U, 4TN8, 4TNO, 4WAB, 4WAU, 4WBQ, 4WBX


• PubMed Abstract: 
  

  We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines.

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Organizational Affiliation: 

Swiss Light Source at Paul Scherrer Institut, Villigen, Switzerland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 17.69 kDa 
• Atom Count: 1,335 
• Modelled Residue Count: 162 
• Deposited Residue Count: 162 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine protease subunit NS2B	A	21	Japanese encephalitis virus strain Nakayama	Mutation(s): 0  Gene Names: NS3
UniProt
Find proteins for P14403 (Japanese encephalitis virus (strain Nakayama)) Explore P14403  Go to UniProtKB:  P14403

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NS3	B	141	Japanese encephalitis virus	Mutation(s): 0  Gene Names: NS3
UniProt
Find proteins for O90417 (Japanese encephalitis virus) Explore O90417  Go to UniProtKB:  O90417

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.218 
• R-Value Work: 0.164 
• R-Value Observed: 0.170 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.26	α = 90
b = 88.26	β = 90
c = 36.22	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Nair, D.T., Weinert, T., Wang, M., Olieric, V.

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2014-12-31
  Changes: Database references, Experimental preparation
• Version 1.2: 2015-01-14
  Changes: Structure summary
• Version 1.3: 2015-08-12
  Changes: Database references
• Version 1.4: 2024-03-20
  Changes: Data collection, Database references, Derived calculations