5F4M Viral Protein date Dec 03, 2015
title Protruding Domain Of Gii.17 Norovirus Kawasaki323
authors B.K.Singh, G.S.Hansman
compound source
Molecule: Capsid Protein
Chain: A, B
Fragment: P Domain (Unp Residues 225-530)
Engineered: Yes
 Organism_scientific: Norovirus 13-Bh-12013gii.17
Organism_taxid: 1508693
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Mbp-Htshp
symmetry Space Group: P 43 21 2
R_factor 0.159 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
121.510 121.510 156.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.27 Å
ligand EDO enzyme
Primary referenceStructural evolution of the emerging 2014/15 GII.17 noroviruses., Singh BK, Koromyslova A, Hefele L, Gurth C, Hansman GS, J Virol. 2015 Dec 23. pii: JVI.03119-15. PMID:26699640
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (208 Kb) [Save to disk]
  • Biological Unit Coordinates (5f4m.pdb1.gz) 201 Kb
  • LPC: Ligand-Protein Contacts for 5F4M
  • CSU: Contacts of Structural Units for 5F4M
  • Structure Factors (1066 Kb)
  • Retrieve 5F4M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5F4M from S2C, [Save to disk]
  • Re-refined 5f4m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5F4M in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 5F4M
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5f4m_B] [5f4m_A] [5f4m]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5F4M
  • Community annotation for 5F4M at PDBWiki (http://pdbwiki.org)

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