1DPS

THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS AND PROTECTS DNA

• PDB DOI: https://doi.org/10.2210/pdb1DPS/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1998-02-23 Released: 1998-09-16 
• Deposition Author(s): Grant, R.A., Filman, D.J., Finkel, S.E., Kolter, R., Hogle, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 

Literature

The crystal structure of Dps, a ferritin homolog that binds and protects DNA.

Grant, R.A., Filman, D.J., Finkel, S.E., Kolter, R., Hogle, J.M.

(1998) Nat Struct Biol 5: 294-303

• PubMed: 9546221 
• DOI: https://doi.org/10.1038/nsb0498-294
• Primary Citation of Related Structures:  
  1DPS


• PubMed Abstract: 
  

  The crystal structure of Dps, a DNA-binding protein from starved E. coli that protects DNA from oxidative damage, has been solved at 1.6 A resolution. The Dps monomer has essentially the same fold as ferritin, which forms a 24-mer with 432 symmetry, a hollow core and pores at the three-fold axes. Dps forms a dodecamer with 23 (tetrahedral) point group symmetry which also has a hollow core and pores at the three-folds. The structure suggests a novel DNA-binding motif and a mechanism for DNA protection based on the sequestration of Fe ions.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 225.11 kDa 
• Atom Count: 16,107 
• Modelled Residue Count: 1,855 
• Deposited Residue Count: 2,004 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DPS	A, B, C, D, E, F, G, H, I, J, K, L	167	Escherichia coli	Mutation(s): 1  Gene Names: DPS EC: 1.16
UniProt
Find proteins for P0ABT2 (Escherichia coli (strain K12)) Explore P0ABT2  Go to UniProtKB:  P0ABT2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth G], T [auth H], U [auth I], V [auth J], W [auth K], X [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.220 
• R-Value Work: 0.188 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.41	α = 90
b = 139.65	β = 90
c = 118.11	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-09-16 
Deposition Author(s): Grant, R.A., Filman, D.J., Finkel, S.E., Kolter, R., Hogle, J.M.

Revision History  

• Version 1.0: 1998-09-16
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations, Other, Structure summary
• Version 1.4: 2024-02-07
  Changes: Data collection