Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Tetrahedral - T  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 23.37 kDa 
• Atom Count: 1448 
• Modelled Residue Count: 166 
• Deposited Residue Count: 211 
• Unique protein chains: 1

2C2J

Crystal Structure Of The Dps92 From Deinococcus Radiodurans

• PDB DOI: 10.2210/pdb2C2J/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Deinococcus radiodurans R1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-29 Released: 2007-02-20 
• Deposition Author(s): Cuypers, M.G., Romao, C.V., Mitchell, E., McSweeney, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Work: 0.179 
• R-Value Observed: 0.179 

Literature

The Crystal Structure of the Dps2 from Deinococcus Radiodurans Reveals an Unusual Pore Profile with a Non-Specific Metal Binding Site.

Cuypers, M.G., Mitchell, E.P., Romao, C.V., Mcsweeney, S.M.

(2007) J Mol Biol 371: 787

• PubMed: 17583727 
• DOI: 10.1016/j.jmb.2006.11.032
• Primary Citation of Related Structures:  
  2C2J, 2C6R


• PubMed Abstract: 
  

The crystal structure of recombinant Dps2 (DRB0092, DNA protecting protein under starved conditions) from the Gram-positive, radiation-resistant bacterium Deinococcus radiodurans has been determined in its apo and iron loaded states. Like other members of the Dps family, the bacterial DrDps2 assembles as a spherical dodecamer with an outer shell diameter of 90 A and an interior diameter of 40 A. A total of five iron sites were located in the iron loaded structure, representing the first stages of iron biomineralisation. Each subunit contains a mononuclear iron ferroxidase centre coordinated by residues highly conserved amongst the Dps family of proteins. In the structures presented, a distinct iron site is observed 6.1 A from the ferroxidase centre with a unique ligand configuration of mono coordination by the protein and no bridging ligand to the ferroxidase centre. A non-specific metallic binding site, suspected to play a regulative role in iron uptake/release from the cage, was found in a pocket located near to the external edge of the C-terminal 3-fold channel.

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Organizational Affiliation: 

ESRF (European Synchrotron Radiation Facility), 6 rue Jules Horowitz, BP 220, 38043 Grenoble, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-BINDING STRESS RESPONSE PROTEIN	A	211	Deinococcus radiodurans R1	Mutation(s): 0  Gene Names: dps2, dps-2, DR_B0092 EC: 1.16
UniProt
Find proteins for Q9RZN1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)) Explore Q9RZN1  Go to UniProtKB:  Q9RZN1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	B [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Work: 0.179 
• R-Value Observed: 0.179 
• Space Group: P 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.453	α = 90
b = 88.453	β = 90
c = 88.453	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-29 
• Released Date: 2007-02-20 
Deposition Author(s): Cuypers, M.G., Romao, C.V., Mitchell, E., McSweeney, S.

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance