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1j6o

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

    Title Crystal structure of TatD-related deoxyribonuclease (TM0667) from Thermotoga maritima at 1.8 A resolution. To be published
    Site JCSG
    PDB Id 1j6o Target Id 282539
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1225,TM0667, 84651 Molecular Weight 29179.67 Da.
    Residues 256 Isoelectric Point 5.23
    Sequence mvdthahlhfhqfdddrnavissfeenniefvvnvgvnledskksldlsktsdrifcsvgvhphdakev pedfiehlekfakdekvvaigetgldffrnispaevqkrvfveqielagklnlplvvhirdayseayei lrteslpekrgvihafssdyewakkfidlgfllgiggpvtypknealrevvkrvgleyivletdcpflp pqpfrgkrnepkylkyvvetisqvlgvpeakvdeattenarriflevke
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.80 Rfree 0.224
    Matthews' coefficent 1.78 Rfactor 0.19
    Waters 195 Solvent Content 30.36

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1j6o
    1. Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage database
    SCH Pegg, SD Brown, S Ojha, J Seffernick - Biochemistry, 2006 - ACS Publications
     
    2. Structural and catalytic diversity within the amidohydrolase superfamily
    CM Seibert, FM Raushel - Biochemistry, 2005 - ACS Publications
     
    3. Assessment of CASP7 predictions in the high accuracy template_based modeling category
    RJ Read, G Chavali - Proteins: Structure, Function, and , 2007 - Wiley Online Library
     
    4. A multi-template combination algorithm for protein comparative modeling
    J Cheng - BMC Structural Biology, 2008 - w01.biomedcentral.com
     
    5. Functional annotation by identification of local surface similarities: a novel tool for structural genomics
    F Ferr, G Ausiello, A Zanzoni - BMC , 2005 - biomedcentral.com
     
    6. Faster data-collection strategies for structure determination using anomalous dispersion
    A Gonzalez - Acta Crystallographica Section D: Biological , 2003 - scripts.iucr.org
     
    7. 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
     
    8. Structural characterization of proteins using residue environments
    SD Mooney, MHP Liang, R DeConde - PROTEINS: Structure, , 2005 - Wiley Online Library
     
    9. The Crystal Structure of a Novel, Latent Dihydroorotase from Aquifex aeolicus at 1.7 Resolution
    PD Martin, C Purcarea, P Zhang, A Vaishnav - Journal of molecular , 2005 - Elsevier
     
    10. 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
     
    11. Efficient recognition of protein fold at low sequence identity by conservative application of Psi_BLAST: application
    FJ Stevens, C Kuemmel, G Babnigg - Journal of Molecular , 2005 - Wiley Online Library
     
    12. Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis
    PJ Silva - Proteins: Structure, Function, and Bioinformatics, 2008 - Wiley Online Library
     
    13. Efficient recognition of protein fold at low sequence identity by conservative application of Psi_BLAST: validation
    FJ Stevens - Journal of Molecular Recognition, 2005 - Wiley Online Library
     
    14. A fold-recognition approach to loop modeling
    C Levefelt, D Lundh - Journal of molecular modeling, 2006 - Springer
     
    15. Widespread distribution of cell defense against D-aminoacyl-tRNAs
    S Wydau, G Van der Rest, C Aubard, P Plateau - Journal of Biological , 2009 - ASBMB
     
    16. Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: II. Case studies and applications
    D Bandyopadhyay, J Huan, J Prins, J Snoeyink - Journal of computer- , 2009 - Springer
     
    17. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     
    18. Valutazione della predizione della struttura proteica: l'iniziativa CASP
    V Thiella - 2010 - tesi.cab.unipd.it
     
    19. Cartographie structurale et fonctionnelle de la liaison entre la peptidyl-ARNt hydrolase et son substrat
    G Laurent - 2010 - hal-polytechnique.archives-ouvertes
     
    20. Proteome-Wide Analyis of Chaperonin-Dependent Protein Folding in Escherichia coli
    T Maier - 2006 - edoc.ub.uni-muenchen.de
     

    Protein Summary


    Thermotoga maritima TM_0667 protein is a TatD-related deoxyribonuclease (PFAM family PF01026), with a classical TIM-like fold, a member of the metallo-dependent hydrolases SCOP superfamily which all share a similar type of distortion of the beta barrel. TM_0667  was the first solved structure from this family, since its deposition in 2002, reveral other related proteins were solved by other SG production centers - 1wxy, 1yix, 1zmm (NYSGXRC) and 2gzx (NECSG)

    Ligand Summary



    References

    Reviews

    References

     

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