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 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 387127
    Molecular Characteristics
    Source Shewanella frigidimarina ncimb 400
    Alias Ids TPS1777,YP_752209.1,, 89080 Molecular Weight 11928.24 Da.
    Residues 101 Isoelectric Point 5.29
    Sequence mqtkvinfndkfslfnqhwsprviaemndyqfklvkvegefvwhehadtdevfivmegtlqiafrdqni tlqagemyvipkgvehkpmakeeckimiiepr
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 5
    Resolution (Å) 2.05 Rfree 0.212
    Matthews' coefficent 2.62 Rfactor 0.186
    Waters 238 Solvent Content 52.99

    Ligand Information


    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

    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.





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