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The Open Protein Structure Annotation Network
PDB Keyword
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1vjx

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

    Title Crystal structure of putative ferritin-like diiron-carboxylate protein (TM1526) from Thermotoga maritima at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 1vjx Target Id 283383
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1297,TM1526, 1.20.1260.10, 282366 Molecular Weight 17192.62 Da.
    Residues 145 Isoelectric Point 4.88
    Sequence mkvsdiltvairleeegerfyrelsehfngeikktfleladqerihaeifrkmsdqenwdevdsylagy afyevfpdtseilrrkdltlkevldiaisvekdsiilyyelkdglvnsdaqktvkkiidqekehlrkll emkrest
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.25652
    Matthews' coefficent 2.80 Rfactor 0.21727
    Waters 60 Solvent Content 55.78

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vjx
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
     
    2. Robust recognition of zinc binding sites in proteins
    JC Ebert, RB Altman - Protein Science, 2008 - Wiley Online Library
     
    3. Exploiting 3D structural templates for detection of metal_binding sites in protein structures
    K Goyal, SC Mande - Proteins: Structure, Function, and , 2008 - Wiley Online Library
     
    4. Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA
    KH Kaminska, U Baraniak, M Boniecki - Proteins: Structure, , 2008 - Wiley Online Library
     
    5. High-throughput protein production for X-ray crystallography and use of size exclusion chromatography to validate or refute computational biological unit predictions
    D McMullan, JM Canaves, K Quijano - Journal of structural and , 2005 - Springer
     
    6. Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii
    EH Lee, HS Kim, HY Kim, YH Jeon - Proteins: Structure, , 2011 - Wiley Online Library
     
    7. Cloning, purification and preliminary X-ray crystallographic analysis of a hypothetical protein, MJ0754, from Methanococcus jannaschii DSM 2661
    EH Lee, KH Nam, KY Hwang - Acta Crystallographica Section F: , 2009 - scripts.iucr.org
     
    8. Modeling the alternative oxidase from the human pathogen Blastocystis using automated hybrid structural template assembly
    DM Standley, M van der Giezen - Research and Reports in , 2012 - dovepress.com
     
    9. Side-chain rotamers in protein _-_ hairpins and a mechanism of their selection
    AM Kargatov, AV Efimov - Molecular Biology, 2007 - Springer
     

    Protein Summary

    The gene TM1526 from Thermotoga maritima encodes the NP_229326 protein, that belongs to the rubrerythrin group (PF02915) and folds into a ferritin-like AB domain found in Archaea and Bacteria COG1528.  Genome context analysis provides a weak hit (score 0.57) with TM1526 neighbors, the endoglucanases celA (TM1524) and celB (TM1525).

     

    SCOP classifies 1vjx inside the all alpha class, ferritin-like (super)family. A Dali structural similarity search with 1vjx as query yields  as top hits: 2fzf (Z-scr=17) and the bacterioferritin 1nfv (Z-scr=16). 

    The protein is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. These proteins were sequenced from mostly anaerobic or microaerophilic metal-metabolizing and/or nitrogen-fixing microbes.  The proteins containing this domain have broad functions. A subfamily of these proteins is known as DPS (DNA Protecting protein under Starved conditions) proteins.  Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide.   

    Ligand Summary



    References

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