3AFP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 

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.,Sect.D 66: 1048-1058

  • DOI: 10.1107/S0907444910032208
  • Primary Citation of Related Structures:  

  • 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 considerab ...

    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.,Sect.D 61: 1140
    • 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.Mol.Biol. 4: 153
    • 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 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.USA 94: 6652


    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-stranded DNA-binding protein
A, B
168Mycobacterium leprae (strain TN)Mutation(s): 0 
Gene Names: ssb
Find proteins for P46390 (Mycobacterium leprae (strain TN))
Go to UniProtKB:  P46390
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.957α = 90.00
b = 78.957β = 90.00
c = 80.213γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
MAR345dtbdata collection
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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