3FXH

Crystal structure from the mobile metagenome of Halifax Harbour Sewage Outfall: Integron Cassette Protein HFX_CASS2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.

Sureshan, V.Deshpande, C.N.Boucher, Y.Koenig, J.E.Stokes, H.W.Harrop, S.J.Curmi, P.M.Mabbutt, B.C.

(2013) PLoS One 8: e52934-e52934

  • DOI: 10.1371/journal.pone.0052934
  • Primary Citation of Related Structures:  
    3FUY, 3FXH, 3FY6, 3IF4, 3IMO, 3JRT

  • PubMed Abstract: 
  • Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty ...

    Mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. In most cases, functional annotation of gene cassettes directly recovered by cassette-PCR is obscured by their characteristically high sequence novelty. This inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. A structural genomics approach incorporating x-ray crystallography has been utilised on a selection of cassettes to investigate evolutionary relationships hidden at the sequence level. Gene cassettes were accessed from marine sediments (pristine and contaminated sites), as well as a range of Vibrio spp. We present six crystal structures, a remarkably high proportion of our survey of soluble proteins, which were found to possess novel folds. These entirely new structures are diverse, encompassing all-α, α+β and α/β fold classes, and many contain clear binding pocket features for small molecule substrates. The new structures emphasise the large repertoire of protein families encoded within the integron cassette metagenome and which remain to be characterised. Oligomeric association is a notable recurring property common to these new integron-derived proteins. In some cases, the protein-protein contact sites utilised in homomeric assembly could instead form suitable contact points for heterogeneous regulator/activator proteins or domains. Such functional features are ideal for a flexible molecular componentry needed to ensure responsive and adaptive bacterial functions.


    Organizational Affiliation

    Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Integron gene cassette protein HFX_CASS2A135uncultured bacteriumMutation(s): 0 
Gene Names: ORF1
UniProt
Find proteins for B0BHE4 (uncultured bacterium)
Explore B0BHE4 
Go to UniProtKB:  B0BHE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0BHE4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.744α = 90
b = 66.829β = 113.52
c = 48.873γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-03-27
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description