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3o8s

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

    Title Crystal structure of an ADP-ribose pyrophosphatase (SSU98_1448) from STREPTOCOCCUS SUIS 89-1591 at 2.27 A resolution. To be published
    Site JCSG
    PDB Id 3o8s Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS6503,YP_001201006.1, 104454
    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 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.43 Rfactor 0.1906
    Waters
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    Solvent Content 49.40

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3o8s
    1. Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement
    TC Terwilliger, RJ Read, PD Adams - Section D: Biological , 2012 - scripts.iucr.org
     

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    Protein Summary

    Pfam update: This sequence hits an N-terminal Nudix_N (PF12535) domain, for which there are no other structures, and a C-terminal NUDIX (PF00293) domain for which there are many structures.

    This target is annotated as an ADP-ribose pyrophosphatase/MutT belonging to the Nudix protein family, Pfam id

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    . This structure was solved by Molecular Replacement using the starting model 2b0v.pdb (Nudix hyrdolase) by Drs. Frank Dimaio & David Baker (Univ of Washington, Seattle).

    Fig1.png

    The structure is similar to that of other Nudix hydrolases (see FFAS link above), but there is no other crystal structure of a similar protein with more than ~25% sequence identity to this target.

    The N-terminus (Gly-0 from the expression tag and residues 1-66 of the target) could not be modeled due to absence of electron density and is missing in the final model. This suggests that the N-terminus is disordered or was cleaved after setting up the crystallization drop. The FFAS list shows that most of this N-terminal region does not align to most other FFAS hits except for PDB id 3e57 and 3dup. This missing N-terminal part of the protein belongs to the Pfam family N-terminal Nudix_N (PF12535) for which no structures are available yet in the PDB.

    A search for other similar structures using EBI SSM results in top hits (Q-score >= 0.5) with PDB ids 3i7u and 3gwy.

    A superimposition of this structure (blue) with that of 2b0v (cyan), 3i7u (magenta) and 3gwy (yellow) is shown:

    Fig2.png

    One of the helices (lower right-hand side in the above figure) is missing in this structure but found in the 2b0v, 3i7u and 3gwy proteins.

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

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     Fig1.png
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    271.9 kB22:26, 14 Jul 2010debanuActions
     Fig2.png
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    458.48 kB22:48, 14 Jul 2010debanuActions
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