Mycobacterium smegmatis Dps tetragonal form

Experimental Data Snapshot

  • Resolution: 2.99 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/10.1016/j.jmb.2004.04.042
  • Primary Citation of Related Structures:  
    1VEI, 1VEL, 1VEQ

  • 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
starvation-induced DNA protecting protein
A, B, C, D, E
A, B, C, D, E, F
183Mycolicibacterium smegmatisMutation(s): 0 
Find proteins for P0C558 (Mycolicibacterium smegmatis)
Explore P0C558 
Go to UniProtKB:  P0C558
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C558
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
K [auth B]
L [auth C]
M [auth C]
G [auth A],
H [auth A],
K [auth B],
L [auth C],
M [auth C],
N [auth D],
O [auth D],
P [auth D],
S [auth E],
T [auth F]
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A],
R [auth D]
O4 S
Query on NA

Download Ideal Coordinates CCD File 
I [auth A],
Q [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.99 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.643α = 90
b = 123.643β = 90
c = 262.328γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description