4R8T

Structure of JEV protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.133 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1038/nmeth.3211
  • Primary Citation of Related Structures:  

  • 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 co ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine protease subunit NS2B
A
21Japanese encephalitis virus (strain Nakayama)Mutation(s): 0 
Find proteins for P14403 (Japanese encephalitis virus (strain Nakayama))
Go to UniProtKB:  P14403
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NS3
B
141Japanese encephalitis virusMutation(s): 0 
Find proteins for O90417 (Japanese encephalitis virus)
Go to UniProtKB:  O90417
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.133 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.164 
  • Space Group: P 62
Unit Cell:
Length (Å)Angle (°)
a = 88.260α = 90.00
b = 88.260β = 90.00
c = 36.220γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata scaling
PHENIXrefinement
d*TREKdata reduction
PHENIXphasing
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2014-12-31
    Type: Database references, Experimental preparation
  • Version 1.2: 2015-01-14
    Type: Structure summary
  • Version 1.3: 2015-08-12
    Type: Database references