1X3E

Crystal structure of the single-stranded DNA-binding protein from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of Mycobacterium smegmatis single-stranded DNA-binding protein and a comparative study involving homologus SSBs: biological implications of structural plasticity and variability in quaternary association.

Saikrishnan, K.Manjunath, G.P.Singh, P.Jeyakanthan, J.Dauter, Z.Sekar, K.Muniyappa, K.Vijayan, M.

(2005) Acta Crystallogr.,Sect.D 61: 1140-1148

  • DOI: 10.1107/S0907444905016896
  • Primary Citation of Related Structures:  
  • Also Cited By: 3AFQ, 3AFP, 3A5U

  • PubMed Abstract: 
  • The structure of Mycobacterium smegmatis single-stranded DNA-binding protein (SSB) has been determined using three data sets collected from related crystals. The structure is similar to that of its homologue from Mycobacterium tuberculosis, indicatin ...

    The structure of Mycobacterium smegmatis single-stranded DNA-binding protein (SSB) has been determined using three data sets collected from related crystals. The structure is similar to that of its homologue from Mycobacterium tuberculosis, indicating that the clamp arrangement that stabilizes the dimer and the ellipsoidal shape of the tetramer are characteristic features of mycobacterial SSBs. The central OB fold is conserved in mycobacterial SSBs as well as those from Escherichia coli, Deinococcus radiodurans and human mitochondria. However, the quaternary structure exhibits considerable variability. The observed plasticity of the subunit is related to this variability. The crystal structures and modelling provide a rationale for the variability. The strand involved in the clamp mechanism, which leads to higher stability of the tetramer, appears to occur in all high-G+C Gram-positive bacteria. The higher stability is perhaps required by these organisms. The mode of DNA binding of mycobacterial SSBs is different from that of E. coli SSB partly on account of the difference in the shape of the tetramers. Another difference between the two modes is that the former contains additional ionic interactions and is more susceptible to salt concentration.


    Related Citations: 
    • Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications
      Saikrishnan, K.,Jeyakanthan, J.,Venkatesh, J.,Acharya, N.,Sekar, K.,Varshney, U.,Vijayan, M.
      (2003) J.Mol.Biol. 331: 385
    • Crystallization and preliminary X-ray studies of the single-stranded DNA-binding protein from Mycobacterium tuberculosis
      Saikrishnan, K.,Jeyakanthan, J.,Venkatesh, J.,Acharya, N.,Purnapatre, K.,Sekar, K.,Varshney, U.,Vijayan, M.
      (2002) Acta Crystallogr.,sect.D 58: 327


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-strand binding protein
A, B
165Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: ssb
Find proteins for Q9AFI5 (Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  Q9AFI5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CD
Query on CD

Download SDF File 
Download CCD File 
A
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.620α = 90.00
b = 78.620β = 90.00
c = 79.834γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-15
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance