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1o1z

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

    Title Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution. Proteins 56 167-170 2004
    Site JCSG
    PDB Id 1o1z Target Id 283478
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1305,TM1621, _0090.002659_, 85091 Molecular Weight 25700.10 Da.
    Residues 222 Isoelectric Point 5.18
    Sequence mivlghrgysakylentleafmkaieagangveldvrlskdgkvvvshdedlkrlfgldvkirdatvse lkeltdgkittlkevfenvsddkiinieikereaadavleiskkrknlifssfdldlldekfkgtkygy lideenygsienfvervekerpyslhvpyqafeleyavevlrsfrkkgivifvwtlndpeiyrkirrei dgvitdevelfvklr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.60 Rfree 0.18
    Matthews' coefficent 2.22 Rfactor 0.139
    Waters 422 Solvent Content 44.16

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1o1z
    1. Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species
    SB Conners, EF Mongodin, MR Johnson - FEMS microbiology , 2006 - Wiley Online Library
     
    2. Real-space protein-model completion: an inverse-kinematics approach
    H Van Den Bedem, I Lotan, JC Latombe - Section D: Biological , 2004 - scripts.iucr.org
     
    3. Active site identification through geometry-based and sequence profile-based calculations: burial of catalytic clefts
    R Greaves, J Warwicker - Journal of molecular biology, 2005 - Elsevier
     
    4. Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases
    MT Murakami, M Freitas Fernandes-Pedrosa - Biochemical and , 2006 - Elsevier
     
    5. A knowledge-driven approach for crystallographic protein model completion
    K Joosten, SX Cohen, P Emsley, W Mooij - Section D: Biological , 2008 - scripts.iucr.org
     
    6. Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins
    R Page, AM Deacon, SA Lesley - Journal of structural and , 2005 - Springer
     
    7. Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 resolution
    E Santelli, R Schwarzenbacher - Proteins: Structure, , 2004 - Wiley Online Library
     
    8. Lateral gene transfer of a dermonecrotic toxin between spiders and bacteria
    MHJ Cordes, GJ Binford - Bioinformatics, 2006 - Oxford Univ Press
     
    9. Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase
    AS Bachmann, FF Duennebier, G Mocz - Gene, 2006 - Elsevier
     
    10. Crystal structure of glycerophosphodiester phosphodiesterase from Agrobacterium tumefaciens by SAD with a large asymmetric unit
    KN Rao, JB Bonanno, SK Burley - Proteins: Structure, , 2006 - Wiley Online Library
     
    11. Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) from Thermoanaerobacter tengcongensis, a metal ion_dependent enzyme: Insight into the
    L Shi, JF Liu, XM An, DC Liang - Proteins: Structure, Function, , 2008 - Wiley Online Library
     
    12. Algorithms exploiting the chain structure of proteins
    I Lotan - 2004 - ai.stanford.edu
     
    13. Computational and Biochemical Analysis of the Xanthomonas Effector AvrBs2 and Its Role in the Modulation of Xanthomonas Type Three Effector Delivery
    B Zhao, D Dahlbeck, KV Krasileva, RW Fong - PLoS , 2011 - dx.plos.org
     
    14. Automated protein model completion: an inverse kinematics approach
    H van den Bedem, I Lotan, JC Latombe - Acta Cryst , 2004 - www-cs-students.stanford.edu
     
    15. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     
    16. Carbohydrate utilization pathway analysis in the hyperthermophile Thermotoga maritima
    SB Conners - 2006 - repository.lib.ncsu.edu
     

    Protein Summary

    The TM1621 gene of Thermotoga maritima encodes a glycerophosphodiester phosphodiesterase (GDPD; EC: 3.1.4.46;  Pfam03009; PubMed:15162496).

    Protein encoded by TM1621 gene has TIM beta/alpha-barrel fold (SCOP sunid:51350) and belongs to family of glycerophosphoryl diester phosphodiesterases (SCOP sunid:89508).


    Ligand Summary



    References

    Reviews

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