1MOJ

Crystal structure of an archaeal dps-homologue from Halobacterium salinarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Iron-oxo clusters biomineralizing on protein surfaces: Structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states.

Zeth, K.Offermann, S.Essen, L.O.Oesterhelt, D.

(2004) Proc.Natl.Acad.Sci.USA 101: 13780-13785

  • DOI: 10.1073/pnas.0401821101
  • Primary Citation of Related Structures:  1TJO, 1TK6, 1TKO, 1TKP

  • PubMed Abstract: 
  • The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake a ...

    The crystal structure of the Dps-like (Dps, DNA-protecting protein during starvation) ferritin protein DpsA from the halophile Halobacterium salinarum was determined with low endogenous iron content at 1.6-A resolution. The mechanism of iron uptake and storage was analyzed in this noncanonical ferritin by three high-resolution structures at successively increasing iron contents. In the high-iron state of the DpsA protein, up to 110 iron atoms were localized in the dodecameric protein complex. For ultimate iron storage, the archaeal ferritin shell comprises iron-binding sites for iron translocation, oxidation, and nucleation. Initial iron-protein interactions occur through acidic residues exposed along the outer surface in proximity to the iron entry pore. This narrow pore permits translocation of ions toward the ferroxidase centers via two discrete steps. Iron oxidation proceeds by transient formation of tri-iron ferroxidase centers. Iron storage by biomineralization inside the ferritin shell occurs at two iron nucleation centers. Here, a single iron atom provides a structural seed for iron-oxide cluster formation. The clusters with up to five iron atoms adopt a geometry that is different from natural biominerals like magnetite but resembles iron clusters so far known only from bioinorganic model compounds.


    Organizational Affiliation

    Department of Membrane Biochemistry, Max Planck Institute for Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dps-like ferritin
A, B, C, D
182Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Gene Names: dps (dpsA)
EC: 1.16.-.-
Find proteins for Q9HMP7 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  Q9HMP7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.147 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.747α = 90.00
b = 90.747β = 90.00
c = 149.410γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-04-20
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance