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The Open Protein Structure Annotation Network
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2pv4

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

    Title Crystal structure of uncharacterized protein (YP_928494.1) from Shewanella amazonensis SB2B at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 2pv4 Target Id 373751
    Molecular Characteristics
    Source Shewanella amazonensis sb2b
    Alias Ids TPS1623,YP_928494.1, BIG_495, 382876 Molecular Weight 16311.57 Da.
    Residues 144 Isoelectric Point 5.08
    Sequence mseidanyralaqqvadkvagrvialdrlpeslltayrslcdelladrdgrftrawdqlpdsasslfer cvfhgfylanawiqlsivardiselqdtdeaiaeqeysglyvrvaeaalkesvkklkkartdrsmynsm revmgi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.95 Rfree 0.250
    Matthews' coefficent 2.53 Rfactor 0.205
    Waters 72 Solvent Content 51.39

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2pv4
    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
     

    Protein Summary

    The Sama_2622 gene from Shewanella amazonensis sb2b encodes the YP_928494 protein of unknown function (DUF3069, PF11269). A search with PSI-BLAST shows Sama_2622 homologs mainly among Shewanella and Vibrio.

    The genetic neighborhood of Sama_2622 homolog, SO3856 ( from Shewanella oneidensis) shows a functional link (score 0.77) with SO3857, a PAP2 family protein (PF01569).

    The 2pv4 structure comprises an all-helical domain that adopts a new fold termed Sama2622-like in which a central helix is surrounded by five others. A DALI search using 2pv4 as query returns no significant hits (Z<5). A search with FATCAT shows the closest structural similarity (rmsd 1.6 Å over 88 residues, 4% sequence identity) with a protein complex involved in membrane fusion (PDB id: 2c5i) (Fridmann-Sirkis 2006) and a putative ferritin-like diiron-carboxylate protein (PDB id: 1vjx) (rmsd 1.4 Å over 115 residues, 5% sequence identity). However, both hits only show alignment along a single helix with insignificant sequence similarity thus not allowing for extrapolations to function.

     

     

    TODO: [look at electrostatic surface, conservation]

    Ligand Summary


    References

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