2V5I Viral Protein date Jul 05, 2007
title Structure Of The Receptor-Binding Protein Of Bacteriophage D Podoviral Tailspike In A Myovirus
authors M.Walter, C.Fiedler, R.Grassl, M.Biebl, R.Rachel, X.L.Hermo-Parra A.L.Llamas-Saiz, R.Seckler, S.Miller, M.J.Van Raaij
compound source
Molecule: Salmonella Typhimurium Db7155 Bacteriophage Det7
Chain: A
Fragment: O-Antigen Binding And Hydrolysis Domain And C-Ter Intertwined Domain, Residues 150-708;
Engineered: Yes
Organism_scientific: Bacteriophage
Organism_taxid: 38018
Strain: Det7
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hms174
Expression_system_variant: De3
Expression_system_plasmid: Pet21a
Other_details: Regensburg Sewage, Germany
symmetry Space Group: H 3 2
R_factor 0.141 R_Free 0.170
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.433 100.433 330.042 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.60 Å
ligand NA enzyme
Primary referenceStructure of the receptor-binding protein of bacteriophage det7: a podoviral tail spike in a myovirus., Walter M, Fiedler C, Grassl R, Biebl M, Rachel R, Hermo-Parrado XL, Llamas-Saiz AL, Seckler R, Miller S, van Raaij MJ, J Virol. 2008 Mar;82(5):2265-73. Epub 2007 Dec 12. PMID:18077713
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (105 Kb) [Save to disk]
  • Biological Unit Coordinates (2v5i.pdb1.gz) 293 Kb
  • LPC: Ligand-Protein Contacts for 2V5I
  • CSU: Contacts of Structural Units for 2V5I
  • Likely Quarternary Molecular Structure file(s) for 2V5I
  • Structure Factors (641 Kb)
  • Retrieve 2V5I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2V5I from S2C, [Save to disk]
  • Re-refined 2v5i structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2V5I 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 2V5I
  • 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
  • 3D motif for 2V5I, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2v5i] [2v5i_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2V5I: [PbH1 ] by SMART
  • Other resources with information on 2V5I
  • Community annotation for 2V5I at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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