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3d82

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

    Title Crystal structure of Domain of Unknown Function with a Cupin Fold (YP_752209.1) from SHEWANELLA FRIGIDIMARINA NCIMB 400 at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 3d82 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1777,YP_752209.1, 2.60.120.10, 89080
    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 5
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.62 Rfactor 0.186
    Waters
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    Solvent Content 52.99

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3d82
    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

    Gene Sfri_3543 from Shewanella frigidimarina NCIMB 400 encodes the YP_752209 protein that folds into a Cupin 2, a conserved barrel domain, and belongs to the PFAM PF07883 (http://pfam.sanger.ac.uk/family?acc=PF07883) family. There are numerous structures available in this family including those listed by pfam.  Additionally, several structurally similar (Dali Z-score provided) proteins have been solved by JCSG and other structural genomics centers and have TOPSAN pages, including: 2oa2 (Z=11), 2ilb (Z=11), 1o4t (Z=11), 1vj2 (Z=12), 2opk (Z=12), 2i45 (Z=17), 2ozj (Z=12), 2pfw (Z=11), and 2pyt (Z=12).

    The residues that in 3d82 coordinate the Ni ion site are: His44, His46, Glu51, and His85, and they are conserved in cupins (see figure 2 and reference 2). An unknown ligand has been observed in some structures (e.g. in 2f4p, Dali Z=10) at the site where UNL has been modeled in this structure.

    3d82 predicted biological unit is a dimer; there are two and a half dimers in the crystallographic asymmetric unit.

    Fig. 1 Biological unit of 3d82 is a dimer. Each chain has a Ni ion and an unknown ligand (UNL) bound to it.


    Figure 2: His44, His46, Glu51, and His85, which coordinate the nickel ion, are shown in hot pink.  Chain A of 3d82 and the nickel ion are shown in green.

    Ligand Summary

    Ni ion and an unknown ligand (UNL) bound to the Ni ion in the active site.

    References

    Reviews

    References

     

    No references found.

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