2YJK Metal Binding Protein date May 19, 2011
title Structure Of Dps From Microbacterium Arborescens In The High
authors K.Zeth, R.Buecheler, W.Boland
compound source
Molecule: Afp
Chain: A, B, C, D, E, F, G, H, I, J, K, L
Synonym: Dps
 Organism_scientific: Microbacterium Arborescens
Organism_taxid: 33883
symmetry Space Group: P 1 21 1
R_factor 0.170 R_Free 0.217
crystal
cell
length a length b length c angle alpha angle beta angle gamma
87.580 92.050 128.580 90.00 96.04 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand FE, OFE enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, J, K, E, B, H, C, D, I, G, L


Primary referenceStructure and Mechanism of Iron Translocation by a Dps Protein from Microbacterium arborescens., Pesek J, Buchler R, Albrecht R, Boland W, Zeth K, J Biol Chem. 2011 Oct 7;286(40):34872-82. Epub 2011 Jul 16. PMID:21768097
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (568 Kb) [Save to disk]
  • Biological Unit Coordinates (2yjk.pdb1.gz) 558 Kb
  • LPC: Ligand-Protein Contacts for 2YJK
  • CSU: Contacts of Structural Units for 2YJK
  • Structure Factors (1806 Kb)
  • Retrieve 2YJK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YJK from S2C, [Save to disk]
  • Re-refined 2yjk structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2YJK 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 2YJK
  • 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 2YJK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yjk_G] [2yjk_J] [2yjk_H] [2yjk_D] [2yjk_L] [2yjk_I] [2yjk_F] [2yjk_B] [2yjk] [2yjk_A] [2yjk_C] [2yjk_E] [2yjk_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 2YJK
  • Community annotation for 2YJK 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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