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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 371505
    Molecular Characteristics
    Source Streptococcus suis 98hah33
    Alias Ids TPS6503,YP_001201006.1, 104454 Molecular Weight 23141.99 Da.
    Residues 205 Isoelectric Point 4.71
    Sequence msqdkwlewavrlqalaqtglaygkdvydmerfeeirqiaaemlvepsgqplevvkdlfcnetgyqtpk ldtraaifqedkillvqendglwslpggwcdvdqsvkdnvvkevkeeagldveaqrvvaildkhknnpa ksahrvtkvfilcrllggefqpnsetvasgffslddlpplylgkntaeqlalcleasrsehwetrfd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.27 Rfree 0.2179
    Matthews' coefficent 2.43 Rfactor 0.1906
    Waters 37 Solvent Content 49.40

    Ligand Information
    Ligands
    Metals

    Jmol

     
    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
     

    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 PFAM:PF00293. 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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    271.9 kB22:26, 14 Jul 2010debanuActions
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    458.48 kB22:48, 14 Jul 2010debanuActions
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