The Open Protein Structure Annotation Network
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    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of putative DNA-binding protein from Caulobacter crescentus at 1.62 A resolution. To be published
    Site JCSG
    PDB Id 1vjf Target Id 355823
    Molecular Characteristics
    Source Caulobacter crescentus cb15
    Alias Ids TPS1351,13421216, RER070207001267 Molecular Weight 18262.15 Da.
    Residues 168 Isoelectric Point 6.14
    Sequence mktradlfaffdahgvdhktldhppvfrveegleikaampgghtknlflkdakgqlwlisalgettidl kklhhvigsgrlsfgpqemmletlgvtpgsvtafglindtekrvrfvldkaladsdpvnfhplkndatt avsqaglrrflaalgvepmivdfaamevvg
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.62 Rfree 0.16673
    Matthews' coefficent 1.87 Rfactor 0.14488
    Waters 176 Solvent Content 33.73

    Ligand Information


    Google Scholar output for 1vjf
    1. The Buccaneer software for automated model building. 1. Tracing protein chains
    K Cowtan - Acta Crystallographica Section D: Biological , 2006 - scripts.iucr.org
    2. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
    3. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination
    S Panjikar, V Parthasarathy, VS Lamzin - Section D: Biological , 2009 - scripts.iucr.org
    4. 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
    5. Structures of Two Bacterial Prolyl-tRNA Synthetases with and without a cis-Editing Domain
    T Crepin, A Yaremchuk, M Tukalo, S Cusack - Structure, 2006 - Elsevier
    6. Quantum Chemical Investigations on Intraresidue Carbonyl_ Carbonyl Contacts in Aspartates of High-Resolution Protein Structures
    TK Pal, R Sankararamakrishnan - The Journal of Physical , 2009 - ACS Publications
    7. Structure of a putative trans-editing enzyme for prolyl-tRNA synthetase from Aeropyrum pernix K1 at 1.7 A resolution
    K Murayama, M Kato-Murayama, K Katsura - Section F: Structural , 2004 - scripts.iucr.org

    Protein Summary

    The gene CC_0111 from Caulobacter crescentus encodes the NP_418930 protein with a putative conserved domain of PrdX deacylase. Its sequence is 58% identical to YP_758156,  an Ala-tRNA(Pro) hydrolase. NP_418930 belongs to the YbaK PF04073 and ProX proteins, and the prolyl-tRNA synthetase-editing domain (ProRS-INS). PrdX deacylase specifically hydrolyzes Ala-tRNA(Pro).

    1vjf belongs to the class of alpha and beta (a+b) proteins and reveals  YbaK/ProRS associated domain fold type SCOP55825. A Dali search with 1vjf provides a top hit (Z-scr=25) with the structure of hypothetical protein ATU3699 from Agrobacterium tumefaciens  1VKI. A second hit (Z-scr=14) with the cysteinyl-tRNA(Pro) deacylase 1dbu.

    Ligand Summary





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