The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of hypothetical protein (YP_561575.1) from Shewanella denitrificans OS-217 at 1.83 A resolution. To be published
    Site JCSG
    PDB Id 2oqm Target Id 368328
    Molecular Characteristics
    Source Shewanella denitrificans os217
    Alias Ids TPS1539,YP_561575.1, BIG_238, BIG_417, 86506 Molecular Weight 19385.24 Da.
    Residues 173 Isoelectric Point 6.07
    Sequence mlydltvvqfskmlknlnaifdkaeafaelkkvdmdvllnsrlaadqfnlirqvqiacdtakvgvarlt gqletapkhddsettlaelrqriasvltylegfseadfanaatiqisqprwqgkyltgyefaiehaipn lyfhittaygilrhngvevgkkdylgampykapil
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.83 Rfree 0.196
    Matthews' coefficent 2.27 Rfactor 0.157
    Waters 553 Solvent Content 45.92

    Ligand Information


    Google Scholar output for 2oqm
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily
    DR Cooper, K Grelewska, CY Kim - Section F: Structural , 2010 - scripts.iucr.org
    3. Dynamic features of homo_dimer interfaces calculated by normal mode analysis
    Y Tsuchiya, K Kinoshita, S Endo, H Wako - Protein Science, 2012 - Wiley Online Library

    Protein Summary


    Gene Sden_0562 from Shewanella denitrificans os-217 encodes the YP_561575 protein from the DUF1993 group (PF09351).

    SCOP classifies 2oqm in the all alpha class, DinB/YfiT-like putative metalloenzymes superfamily. DALI returns as top hits the APC36150 protein PDB:3e4x (Z=13), the DinB-like protein PDB:3dka (Z=12), and the YIZA protein PDB:2qe9 (Z=11).

    The structure of 2oqm proved to be particularly valuable because it identified a subfamily of 170 unique sequences to the DinB superfamily that were not distinguished using the sequence of any other structure. This subfamily lacks the presumed active site residues, suggesting that the superfamily has acquired functions beyond its catalytic role. This is seen for many enzyme families and usually means that the protein has assumed a binding role in place of a catalytic one. In this subfamily the C-terminal helix that normally contains two of the active site histidines is the most conserved region supporting a potential binding role.


    Ligand Summary





    No references found.

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