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 (JCVI_PEP_1096688149193) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.79 A resolution. To be published
    Site JCSG
    PDB Id 2od5 Target Id 367491
    Molecular Characteristics
    Alias Ids TPS1513,JCVI_PEP_1096688149193, 430153 Molecular Weight 12969.09 Da.
    Residues 115 Isoelectric Point 5.94
    Sequence mtgavetesmktvrirekikkflgdrprntaeilehinstmrhgttsqqlgnvlskdkdivkvgyikrs gilsggydicewatrnwvaehcpewtegqpiilneegdftlgplpe
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.79 Rfree 0.213
    Matthews' coefficent 3.02 Rfactor 0.189
    Waters 77 Solvent Content 59.33

    Ligand Information


    Google Scholar output for 2od5
    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. Probing metagenomics by rapid cluster analysis of very large datasets
    W Li, JC Wooley, A Godzik - PLoS One, 2008 - dx.plos.org
    3. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer

    Protein Summary

    The gene ID JCVI_PEP_1096688149193 from an ocean metagenomics sample encodes a hypothetical protein of unknown function.  This is one of the six structures solved from synthetic genes that were based on ORFs identified in the GOS project [Ref].


    No significant sequence similarity to known proteins from known genomes, save similarities to other GOS ORFs.  The fold type assignment suggests  DNA/RNA-binding 3-helical bundle SCOP46688, connecting this protein with the  "Winged helix" DNA-binding domain superfamily.  This domain is associated with transcription factors.

    Ligand Summary





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