2XD8 Virus date Apr 30, 2010
title Capsid Structure Of The Infectious Prochlorococcus Cyanophag
authors X.Liu, Q.Zhang, K.Murata, M.L.Baker, M.B.Sullivan, C.Fu, M.Dougher M.F.Schmid, M.S.Osburne, S.W.Chisholm, W.Chiu
compound source
Molecule: T7-Like Capsid Protein
Chain: A, B, C, D, E, F, G
Synonym: Gp10
Engineered: Yes
 Organism_scientific: Prochlorococcus Phage P-Ssp7
Organism_taxid: 268748
Expression_system: Prochlorococcus Med4
Expression_system_taxid: 1220
Other_details: P-Ssp7 Were Propagated On Prochlorococcus Me
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.60 Å
Primary referenceStructural changes in a marine podovirus associated with release of its genome into Prochlorococcus., Liu X, Zhang Q, Murata K, Baker ML, Sullivan MB, Fu C, Dougherty MT, Schmid MF, Osburne MS, Chisholm SW, Chiu W, Nat Struct Mol Biol. 2010 Jul;17(7):830-6. Epub 2010 Jun 13. PMID:20543830
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (51 Kb) [Save to disk]
  • Biological Unit Coordinates (2xd8.pdb1.gz) 2773 Kb
  • CSU: Contacts of Structural Units for 2XD8
  • Retrieve 2XD8 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2XD8 from S2C, [Save to disk]
    • View 2XD8 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 2XD8
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2XD8, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2xd8_F] [2xd8_D] [2xd8] [2xd8_C] [2xd8_A] [2xd8_G] [2xd8_E] [2xd8_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2XD8
  • Community annotation for 2XD8 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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