4A25

X-ray structure Dps from Kineococcus radiotolerans in complex with Mn (II) ions.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Kineococcus Radiotolerans Dps Forms a Heteronuclear Mn-Fe Ferroxidase Center that May Explain the Mn-Dependent Protection Against Oxidative Stress.

Ardini, M.Fiorillo, A.Fittipaldi, M.Stefanini, S.Gatteschi, D.Llari, A.Chiancone, E.

(2013) Biochim Biophys Acta 1830: 3745

  • DOI: https://doi.org/10.1016/j.bbagen.2013.02.003
  • Primary Citation of Related Structures:  
    4A25

  • PubMed Abstract: 

    The ferroxidase center of DNA-binding protein from starved cells (Dps) is a major player in the iron oxidation/detoxification process that leads to a decreased reactive oxygen species production. The possible Mn(II) participation in this process has been studied in Dps from Kineococcus radiotolerans, a radiation-resistant bacterium with a high cytosolic Mn/Fe ratio and a high capacity to survive ionizing and stress conditions.


  • Organizational Affiliation

    Department of Biochemical Sciences A. Rossi Fanelli, Sapienza University of Rome, Italy.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FERRITIN DPS FAMILY PROTEIN
A, B, C, D
169Kineococcus radiotoleransMutation(s): 0 
UniProt
Find proteins for A6WG04 (Kineococcus radiotolerans (strain ATCC BAA-149 / DSM 14245 / SRS30216))
Explore A6WG04 
Go to UniProtKB:  A6WG04
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6WG04
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
O [auth C],
Q [auth D],
R [auth D],
S [auth D]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
M [auth B]
N [auth B]
P [auth C]
I [auth A],
J [auth A],
M [auth B],
N [auth B],
P [auth C],
T [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.474α = 90
b = 150.474β = 90
c = 86.618γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2013-02-20
    Changes: Database references
  • Version 1.2: 2013-05-15
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description