Crystal structure of putative metal-dependent hydrolase APC36150

Experimental Data Snapshot

  • Resolution: 2.51 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.

Cooper, D.R.Grelewska, K.Kim, C.Y.Joachimiak, A.Derewenda, Z.S.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 219-224

  • DOI: https://doi.org/10.1107/S1744309109053913
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of the dinB gene product from Geobacillus stearothermophilus (GsDinB) is reported at 2.5 A resolution. The dinB gene is one of the DNA-damage-induced genes and the corresponding protein, DinB, is the founding member of a Pfam family with no known function. The protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme MDMPI (mycothiol-dependent maleylpyruvate isomerase), YfiT and TTHA0303, a member of a small DUF (domain of unknown function). However, a search of the DALI structural database revealed similarities to a further 11 new unpublished structures contributed by structural genomics centers. The sequences of these proteins are quite divergent and represent several Pfam families, yet their structures are quite similar and most (but not all) seem to have the ability to coordinate a metal ion using a conserved histidine-triad motif. The structural similarities of these diverse proteins suggest that a new Pfam clan encompassing the families that share this fold should be created. The proteins that share this fold exhibit four different quaternary structures: monomeric and three different dimeric forms.

  • Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative metal-dependent hydrolase
A, B, C, D
157Geobacillus stearothermophilusMutation(s): 0 
Find proteins for D0VX25 (Geobacillus stearothermophilus)
Explore D0VX25 
Go to UniProtKB:  D0VX25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VX25
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.51 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.477α = 90
b = 71.47β = 90
c = 123.256γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description