4TPL

West Nile Virus Non-structural protein 1 (NS1) Form 1 crystal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history

Literature

Use of massively multiple merged data for low-resolution S-SAD phasing and refinement of flavivirus NS1.

Akey, D.L.Brown, W.C.Konwerski, J.R.Ogata, C.M.Smith, J.L.

(2014) Acta Crystallogr.,Sect.D 70: 2719-2729

  • DOI: 10.1107/S1399004714017556

  • PubMed Abstract: 
  • An emergent challenge in macromolecular crystallography is the identification of the substructure from native anomalous scatterers in crystals that diffract to low to moderate resolution. Increasing the multiplicity of data sets has been shown to mak ...

    An emergent challenge in macromolecular crystallography is the identification of the substructure from native anomalous scatterers in crystals that diffract to low to moderate resolution. Increasing the multiplicity of data sets has been shown to make previously intractable phasing problems solvable and to increase the useful resolution in model refinement. For the West Nile virus nonstructural protein 1 (NS1), a protein of novel fold, the utility of exceptionally high multiplicity data is demonstrated both in solving the crystal structure from the anomalous scattering of the native S atoms and in extending the useful limits of resolution during refinement. A high-multiplicity data set from 18 crystals had sufficient anomalous signal to identify sulfur sites using data to 5.2 Å resolution. Phases calculated to 4.5 Å resolution and extended to 3.0 Å resolution were of sufficient quality for automated building of three-quarters of the final structure. Crystallographic refinement to 2.9 Å resolution proceeded smoothly, justifying the increase in resolution that was made possible by combining multiple data sets. The identification and exclusion of data from outlier crystals is shown to result in more robust substructure determination.


    Related Citations: 
    • Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system.
      Akey, D.L.,Brown, W.C.,Dutta, S.,Konwerski, J.,Jose, J.,Jurkiw, T.J.,DelProposto, J.,Ogata, C.M.,Skiniotis, G.,Kuhn, R.J.,Smith, J.L.
      (2014) Science --: 881


    Organizational Affiliation

    Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109-2216, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
West Nile Virus NS1
A, B
377West Nile virusMutation(s): 0 
Find proteins for Q5SBG8 (West Nile virus)
Go to UniProtKB:  Q5SBG8
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MAN
Query on MAN

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Download CCD File 
B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
OXN
Query on OXN

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Download CCD File 
A, B
OXTOXYNOL-10
ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL); TRITON X-100
C34 H62 O11
IVKNZCBNXPYYKL-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

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Download CCD File 
B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.170 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 167.850α = 90.00
b = 167.850β = 90.00
c = 93.730γ = 120.00
Software Package:
Software NamePurpose
SHELXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
SHELXDphasing
Cootmodel building
DMphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesP01AI055672

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-12-24
    Type: Database references
  • Version 1.2: 2015-02-25
    Type: Derived calculations
  • Version 2.0: 2017-09-06
    Type: Advisory, Atomic model, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
  • Version 2.1: 2017-11-22
    Type: Refinement description