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3g16

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

    Title Crystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution. To be published
    Site JCSG
    PDB Id 3g16 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS20868,YP_001022489.1, 3.10.450.50, 325168
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.56 Rfactor 0.148
    Waters
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    Solvent Content 51.87

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3g16
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

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    Protein Summary

    Pfam update: This overlaps with the relatively new family SnoaL_2 of proteins, sharing the SnoaL fold..

    The crystal structure reveals it to be a ketosteroid isomerase-like protein.

    It is present as a dimer in the crystal structure and crystal packing analysis suggests that this dimer should be the stable oligomeric form in solution. An unidentified ligand (UNL, orange spheres) has been modeled at the putative active site in both protomers. It is possible that this UNL is actually a MES molecule from the crystallization buffer (see ligand summary below).

    Fig1.jpg

    The final UNL superimposed on a Fo-Fc omit electron density map (green) is shown here:

    Fig2.jpg

    There are numerous interesting residues (green sticks) in this putative active site around the UNL which could be

    functionally important. They are: Tyr18, Tyr19, Cys22, His40, Phe42, Tyr47, Trp61, Trp72, Trp90, His92, Glu105 and Tyr123.

    Fig3.jpg

     

    Other protein structures that are most similar in structure (by SSM at EBI) to this protein are (PDB ids): 1tuh, 2z77, 1w02, 1e97, etc. These are ketosteroid isomerase like proteins. Other similar proteins based on sequence can be found via the BLAST and FFAS links above and conserved residues can be seen.

    Tyr18 is found to be conserved in several of these other proteins.

    Ligand Summary

    UNL (Unidentified Ligand) at the putative active site.

    It is possible that this UNL is actually a partially occupied MES from the crystallization buffer.

    THIS INFERENCE IS BASED ON THE LOWER B-FACTOR OF ATOM O7 OF UNL-1 WHICH
    SUGGESTS THAT THIS MAY BE A HEAVIER ATOM (LIKE SULFUR).

    Reviews

    References

     

    No references found.

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