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The Open Protein Structure Annotation Network
PDB Keyword
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3m1t

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

    Title Crystal structure of Putative phosphohydrolase (YP_929327.1) from Shewanella amazonensis SB2B at 1.62 A resolution. To be Published
    Site JCSG
    PDB Id 3m1t Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS26607,YP_929327.1, _0037.000821_, 326250
    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 2.93 Rfactor 0.182
    Waters
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    Solvent Content 57.98

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3m1t

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    Protein Summary

    [The following content, including  figures, is uploaded from Kevin Kai Jin's refinement summary, more discussion about this protein structure will be available very soon]

     

    Pfam:  matches the Pfam HDOD (PF08668) entry

     

    Gene Sama_3455 from SHEWANELLA AMAZONENSIS SB2 encodes the YP_929327 protein, which belongs to the pfam PF08668  group with members displaying phosphohydrolase activity.  The NCBI blast sequence alignment indicates that this protein contains a conserved domain belonging to HD superfamily.  

    Pre-SCOP classifies 3m1t in the all alpha class, HD-domain/PDEase-like superfamily, modified HD domain family. A structural similarity search via SSM and Dali sever show that 3m1t is structurally similar to the exopolyphosphatase (PDB 2FLO),  a putative phosphohydrolase (JCSG target PDB 3I7A) and metal-dependent phosphohydrolase (JCSG target PDB 3HC1). Differing from structure 3HC1, the corresponding residues in protein YP_929327 are varied and no metal ions are identified in the structure.  The interface interaction suggests that the biomolecule of 3m1t is likely a dimer.

    394107_1.png

     

    Figure 1. The structure of 3m1t mainly consists of helices.

     

     

    394107_2.png

     

     

    Figure 2. The probable biomolecule of 3m1t is a dimer.

     

    394107_3.png

    Figure 3. Protein 3M1T (Green) is structurally similar

    to 3HC1(cyan), and 3I7A(magenta). 
     

     

    394107_5.png

    Figure 4. Protein 3HC1(JCSG target) is a metal-(Fe)-dependent

    phosphohdyrolase.
     

     

    394107_4.png

     

    Figure 5. Corresponding metal binding site is mutated in 3m1t.
     

    Ligand Summary

    Reviews

    References

     

    No references found.

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