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The Open Protein Structure Annotation Network
PDB Keyword
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3di5

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

    Title Crystal structure of a DinB-like Protein (NP_980948.1) from BACILLUS CEREUS ATCC 10987 at 2.01 A resolution. To be published
    Site JCSG
    PDB Id 3di5 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS9372,NP_980948.1, PF05163, 91674
    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 2.16 Rfactor 0.229
    Waters
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    Solvent Content 43.04

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3di5
    1. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily
    DR Cooper, K Grelewska, CY Kim - Section F: Structural , 2010 - scripts.iucr.org
     
    2. A New Library of Surface Patches: Design and Applications
    R Gamliel, K Kedem, R Kolodny, C Keasar - 2009 - cs.bgu.ac.il
     

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    Protein Summary

    The BCE_4655 gene from Bacillus cereus atcc 10987 encodes a damage-inducible (DinB) protein (PF05163).

    3di5 adopts a DinB/YfiT-like putative metalloenzymes fold and shows significant similarity (DALI Z-score=14-11) to other structures solved by structural genomics (PDB ids:

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    ,
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    ,
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    ,
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    ,
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    ,
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    ).

    YfiT has been proposed to function as a metal-dependent hydrolase [Ref] and has been deposited with PDB as

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    (Z=12). A comparison between 1rxq and 3di5 reveals that the proteins share the Ni metal binding site, putting more confidence into the prediction of a metal-dependent hydrolase.

    3di5-1rxq-superpos.png

    Structure superposition showing equivalent residues of 3di5 (red) and 1rxq (orange) with their Ni ions (dark grey and light grey for 3di5 and 1rxq, respectively). The Ni ligation site contains three histidine residues (H48, H127, H131) and is strictly conserved. Another aspartate residue from 1rxq shown in green is not present in 3di5, but its relevance is questionable since it is separated by about 4A from the metal.

     

    To do: Phylogenetic analysis?

    Ligand Summary

    Reviews

    References

     

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     3di5-1rxq-superpos.png
    Structure superposition between 3di5 and 1rxq
    241.71 kB20:04, 3 Mar 2010chrisxActions
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