Experimental Data Snapshot

  • Resolution: 3.35 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 

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Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG.

Saikrishnan, K.Bidya Sagar, M.Ravishankar, R.Roy, S.Purnapatre, K.Handa, P.Varshney, U.Vijayan, M.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1269-1276

  • DOI: https://doi.org/10.1107/s0907444902009599
  • Primary Citation of Related Structures:  
    1LQG, 1LQJ, 1LQM

  • PubMed Abstract: 

    The structures of a new crystal form of free Escherichia coli uracil DNA glycosylase (UDG), containing four molecules in the asymmetric unit, and two forms of its complex with the proteinaceous inhibitor Ugi, containing two and four crystallographically independent complexes, have been determined. A comparison of these structures and the already known crystal structures containing UDG shows that the enzyme can be considered to be made up of two independently moving structural entities or domains. A detailed study of free and DNA-bound human enzyme strengthens this conclusion. The domains close upon binding to uracil-containing DNA, whereas they do not appear to do so upon binding to Ugi. The comparative study also shows that the mobility of the molecule involves the rigid-body movement of the domains superposed on flexibility within domains.

  • 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
A, B, C, D
229Escherichia coliMutation(s): 0 
EC: 3.2.2
Find proteins for P12295 (Escherichia coli (strain K12))
Explore P12295 
Go to UniProtKB:  P12295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12295
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.35 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.241 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.21α = 90
b = 125.21β = 90
c = 90.047γ = 120
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: 2002-11-10
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Refinement description