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 hypothetical protein (ATU3699) from Agrobacterium tumefaciens at 1.60 A resolution. To be published
    Site JCSG
    PDB Id 1vki Target Id 354222
    Molecular Characteristics
    Source Agrobacterium tumefaciens str. c58
    Alias Ids TPS1325,15159614, RER070207001267 Molecular Weight 18566.08 Da.
    Residues 169 Isoelectric Point 5.51
    Sequence mtensrktatelfefldglgishttkqhepvftvaesqslrdlipgghtknlfvkdkkdqyfvltveen avvdlksvhktigaasrvsfgrpekmleylgvvpgsvtvfgaindtarqvtfvldsdllenelvnghpl sndqtttiaskdlirfleatghaplvlkvse
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.60 Rfree 0.18496
    Matthews' coefficent 2.02 Rfactor 0.15201
    Waters 510 Solvent Content 38.78

    Ligand Information


    Google Scholar output for 1vki
    1. Protein function prediction using local 3D templates
    RA Laskowski, JD Watson, JM Thornton - Journal of Molecular Biology, 2005 - Elsevier
    2. 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
    3. 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
    4. Efficient protein tertiary structure retrievals and classifications using content based comparison algorithms
    PH Chi - 2007 - mospace.umsystem.edu
    5. 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
    6. CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology
    A Paiardini, F Bossa, S Pascarella - Nucleic acids research, 2005 - Oxford Univ Press

    Protein Summary

    The gene Atu3699 (or AGR_L_2275) from Agrobacterium tumefaciens encodes the NP_356919, a putative conserved domain of the PrdX deacylase.  The PrdX protein is a homolog of the YbaK and ProX proteins (PF04073), and the prolyl-tRNA synthetase-editing domain (ProRS-INS). PrdX deacylases specifically hydrolyze Ala-tRNA(Pro).

    The 1vki structure belongs to the class of alpha and beta (a+b) proteins and reveals  YbaK/ProRS associated domain fold type SCOP55825, inside the YbaK/ProRS (super)family. The structure of a close homologue of this protein from Caulobacter crescentus has been solved, 1VJF (Z=26). Other similar structures include the APE2540 protein 1wdv (Z=16), the cysteinyl-tRNA(Pro) deacylase 1dbu (Z=16), and the TTHA1699 protein 2z0x (Z=15).

    Ligand Summary





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