4R8T

Structure of JEV protease


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 

wwPDB Validation   3D Report Full Report


This is version 1.4 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: 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.


  • Organizational Affiliation

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


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease subunit NS2B21Japanese encephalitis virus strain NakayamaMutation(s): 0 
Gene Names: NS3
UniProt
Find proteins for P14403 (Japanese encephalitis virus (strain Nakayama))
Explore P14403 
Go to UniProtKB:  P14403
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14403
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NS3141Japanese encephalitis virusMutation(s): 0 
Gene Names: NS3
UniProt
Find proteins for O90417 (Japanese encephalitis virus)
Explore O90417 
Go to UniProtKB:  O90417
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO90417
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
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 = 88.26α = 90
b = 88.26β = 90
c = 36.22γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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