Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 20.51 kDa 
• Atom Count: 1395 
• Residue Count: 175 
• Unique protein chains: 1

1VEI

Mycobacterium smegmatis Dps

• DOI: 10.2210/pdb1VEI/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycolicibacterium smegmatis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-03-31 Released: 2004-06-29 
• Deposition Author(s): Roy, S., Gupta, S., Das, S., Sekar, K., Chatterji, D., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

X-ray Analysis of Mycobacterium smegmatis Dps and a Comparative Study Involving Other Dps and Dps-like Molecules

Roy, S., Gupta, S., Das, S., Sekar, K., Chatterji, D., Vijayan, M.

(2004) J Mol Biol 339: 1103-1113

• PubMed: 15178251 
• DOI: 10.1016/j.jmb.2004.04.042
• Primary Citation of Related Structures:  
  1VEQ, 1VEL, 1VEI


• PubMed Abstract: 
  

The structure of the DNA binding protein from starved cells from Mycobacterium smegmatis has been determined in three crystal forms and has been compared with those of similar proteins from other sources. The dodecameric molecule can be described as a distorted icosahedron. The interfaces among subunits are such that the dodecameric molecule appears to have been made up of stable trimers. The situation is similar in the proteins from Escherichia coli and Agrobacterium tumefaciens, which are closer to the M.smegmatis protein in sequence and structure than those from other sources, which appear to form a dimer first. Trimerisation is aided in the three proteins by the additional N-terminal stretches that they possess. The M.smegmatis protein has an additional C-terminal stretch compared to other related proteins. The stretch, known to be involved in DNA binding, is situated on the surface of the molecule. A comparison of the available structures permits a delineation of the rigid and flexible regions in the molecule. The subunit interfaces around the molecular dyads, where the ferroxidation centres are located, are relatively rigid. Regions in the vicinity of the acidic holes centred around molecular 3-fold axes, are relatively flexible. So are the DNA binding regions. The crystal structures of the protein from M.smegmatis confirm that DNA molecules can occupy spaces within the crystal without disturbing the arrangement of the protein molecules. However, contrary to earlier suggestions, the spaces do not need to be between layers of protein molecules. The cubic form provides an arrangement in which grooves, which could hold DNA molecules, criss-cross the crystal.

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Organizational Affiliation: 

Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
starvation-induced DNA protecting protein	A	183	Mycolicibacterium smegmatis	Mutation(s): 0  Gene Names: dps EC: 1.16
Find proteins for P0C558 (Mycolicibacterium smegmatis) Explore P0C558  Go to UniProtKB:  P0C558

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
FE	A	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.250 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: F 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.965	α = 90
b = 179.965	β = 90
c = 179.965	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-31 
• Released Date: 2004-06-29 
Deposition Author(s): Roy, S., Gupta, S., Das, S., Sekar, K., Chatterji, D., Vijayan, M.

Revision History 

• Version 1.0: 2004-06-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance