3AFQ

Crystal structure of the single-stranded DNA binding protein from Mycobacterium leprae (Form II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray and molecular-dynamics studies on Mycobacterium leprae single-stranded DNA-binding protein and comparison with other eubacterial SSB structures

Kaushal, P.S.Singh, P.Sharma, A.Muniyappa, K.Vijayan, M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 1048-1058

  • DOI: 10.1107/S0907444910032208
  • Primary Citation of Related Structures:  
    3AFP, 3AFQ

  • PubMed Abstract: 
  • The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 Å resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable v ...

    The crystal structures of two forms of Mycobacterium leprae single-stranded DNA-binding protein (SSB) have been determined at 2.05 and 2.8 Å resolution. Comparison of these structures with the structures of other eubacterial SSBs indicates considerable variation in their quaternary association, although the DNA-binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but could be related to variation in protein stability. Molecular-dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype Escherichia coli SSB and the individual subunits of both proteins. Together, the X-ray studies and molecular-dynamics simulations yield information on the relatively rigid and flexible regions of the molecule and on the effect of oligomerization on flexibility. The simulations provide insight into the changes in subunit structure on oligomerization. They also provide insight into the stability and time evolution of the hydrogen bonds/water bridges that connect the two pairs of monomers in the tetramer.


    Related Citations: 
    • 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 D Biol Crystallogr 61: 1140
    • 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
    • Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution
      Yang, C., Curth, U., Urbanke, C., Kang, C.
      (1997) Nat Struct Biol 4: 153
    • Crystal structure of the homo-tetrameric DNA binding domain of Escherichia coli single-stranded DNA-binding protein determined by multiwavelength x-ray diffraction on the selenomethionyl protein at 2.9-A resolution
      Raghunathan, S., Ricard, C.S., Lohman, T.M., Waksman, G.
      (1997) Proc Natl Acad Sci U S A 94: 6652

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Single-stranded DNA-binding protein ABCD168Mycobacterium leprae TNMutation(s): 0 
Gene Names: ssbML2684MLCB1913.20c
Find proteins for P46390 (Mycobacterium leprae (strain TN))
Explore P46390 
Go to UniProtKB:  P46390
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.486α = 90
b = 102.486β = 90
c = 120.762γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASESphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-04
    Changes: Database references, Derived calculations