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The Open Protein Structure Annotation Network
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3fsd

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

    Title Crystal structure of NTF2-like protein of unknown function in nutrient uptake (YP_427473.1) from RHODOSPIRILLUM RUBRUM ATCC 11170 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3fsd Target Id 378192
    Molecular Characteristics
    Source Rhodospirillum rubrum atcc 11170
    Alias Ids TPS7054,YP_427473.1, 3.10.450.50, 335802 Molecular Weight 14443.75 Da.
    Residues 133 Isoelectric Point 6.28
    Sequence msnalatlaspaddiafyeerlraamltgdlkgletlladdlafvdhtgcvktkqthlepyragllkls rldlsdavvraagedgrvvvvravtagvydgeaftetlrftriwrrtqgpagwklvaghcsvil
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.221
    Matthews' coefficent Rfactor 0.172
    Waters 94 Solvent Content

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fsd
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Pfam update: SnoaL_2 family,  PF12680.

    This is a protein of unknown function.

    It is a monomer in the asymmetric unit of the unit cell in the crystal structure:

    Fig1.png

    Crystal lattice packing analysis suggests that the stable oligomeric form in solution should be a dimer. Analytical size exclusion chromatography in combination with static light scattering support the assignment of a dimer as the significant oligomeric form in solution:

    Fig2-1.png

    An unidentified ligand (UNL) has been modeled in what appears to be the putative active site surrounded by the residues Cys129 (blue) and Phe109, His47, His57, Phe44, Phe103, Glu105, Tyr98 and Val66:

    Fig3.png

    The UNL in a Fo-Fc map at 3.0 sigma (green) calculated by omitting the ligand (2Fo-Fc map in blue at 1.0 sigma) shows the fit of the  ligand in the electron density:

    Fig4.jpg

    Other proteins of similar structure (using the Protein structure comparison service SSM at European Bioinformatics Institute (http://www.ebi.ac.uk/msd-srv/ssm), authored by E. Krissinel and K. Henrick) are various other NTF2-like proteins with the most similar being the NTF2-like protein of unknown function from C. hutchinsonii (PDB id 2r4i) with a Q-score of 0.83, rmsd=1.21A and 33% sequence identity over 117 Calpha residues, also solved by the JCSG, Topsan

    Based on the structure, Cys129 is likely to be involved in the biochemistry of this protein.

    Ligand Summary

    UNL (Unidentified Ligand)

    Reviews

    References

     

    No references found.

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