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3in6

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

    Title Crystal structure of FMN-binding protein (YP_752906.1) from Syntrophomonas wolfei str. Goettingen at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3in6 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS20817,SWOL_07JAN05_CONTIG119_REVISED_GENE619, 2.30.110.10, 87239
    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 2
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.31 Rfactor 0.219
    Waters
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    Solvent Content 46.79

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3in6
    1. The structure of a Xanthomonas general stress protein involved in citrus canker reveals its flavin-binding property
    E Hilario, Y Li, D Niks, L Fan - Acta Crystallographica Section D: , 2012 - scripts.iucr.org
     

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    Protein Summary

    Pfam update: family Pyridox_oxidase, PF01243.

    The gene Swol_0183 from Syntrophomonas wolfei str. goettingen encodes the YP_752906 protein. As there is no Pfam classification for this protein yet, it is difficult to speculate on possible function of this protein. A sequence search against the Pfam database shows that it may be related to the family PF01243 (Pyridoxamine 5-phosphate oxidase, very weak sequence similarity with e-value=0.54). [Actually, HHPred gives a very high probability of association with PF01243 (99.6%) with E-value 3.9E-14, P-value 3.8E-18 over the first 100 residues.]

    Pre-SCOP classifies 3in6 in the FMN-binding split barrel superfamily. 3in6 protein crystallizes as a dimer. A flavin mononucleotide (FMN) molecule has been modeled in the structure (yellow sticks):

    Fig1.png

    Both FFAS and structural comparisons using SSM reveal significant hits with other FMN binding proteins, for example, PDB ids 2htd (Z=13), 1axj (Z=12)(Ref1), 2q9k(Z=10). The 2htd and 2q9k are structures of proteins of unknown function and have also been solved at the JCSG (target id 367187 and 375036).

     

    A superimposition of the 3in6 structure (red) with that of the 1axj (cyan) reveals their structural similarity (2.3A rmsd over 114 Ca residues) despite an overall sequence identity of only ~15%. The FMN bound in the 1axj structure (magenta) is also in the same location as found in the 3in6 structure but the protein residues involved in ligand interaction/FMN-binding pocket are not conserved, except for a few.

    FN12456A_1axj.png

    References:

    1. Pathway of chymotrypsin evolution suggested by the structure of the FMN-binding protein from Desulfovibrio vulgaris (Miyazaki F)

    Ligand Summary

    Flavin mononucleotide (FMN) that probably co-purified with the protein has been modeled.

    Reviews

    References

     

    No references found.

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     Fig1.png
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    216.16 kB22:43, 27 May 2009debanuActions
     FN12456A_1axj.png
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    249.28 kB18:43, 2 Jul 2009debanuActions
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