Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 35.07 kDa 
• Atom Count: 1802 
• Residue Count: 222 
• Unique protein chains: 1

1X3F

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

• DOI: 10.2210/pdb1X3F/pdb

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


• Deposited: 2005-05-05 Released: 2005-08-15 
• Deposition Author(s): Saikrishnan, K., Manjunath, G.P., Singh, P., Jeyakanthan, J., Dauter, Z., Sekar, K., Muniyappa, K., Vijayan, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.200 
• R-Value Observed: 0.208 

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 D Biol Crystallogr 61: 1140-1148

• PubMed: 16041080 
• DOI: 10.1107/S0907444905016896
• Primary Citation of Related Structures:  
  1X3G, 1X3F, 1X3E


• 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, 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.

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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 D Biol Crystallogr 58: 327

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-strand binding protein	A, B	165	Mycolicibacterium smegmatis	Mutation(s): 0
Find proteins for Q9AFI5 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore Q9AFI5  Go to UniProtKB:  Q9AFI5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	A, B	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.200 
• R-Value Observed: 0.208 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.014	α = 90
b = 78.014	β = 90
c = 71.018	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-05 
• Released Date: 2005-08-15 
Deposition Author(s): Saikrishnan, K., Manjunath, G.P., Singh, P., Jeyakanthan, J., Dauter, Z., Sekar, K., Muniyappa, K., Vijayan, M.

Revision History 

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