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3ge6

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

    Title Crystal structure of putative nitroreductase in complex with FMN (YP_001815433.1) from EXIGUOBACTERIUM SP. 255-15 at 1.85 A resolution. To be published
    Site JCSG
    PDB Id 3ge6 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS18288,YP_001815433.1, 3.40.109.10, 85563
    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 2.14 Rfactor 0.169
    Waters
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    Solvent Content 42.65

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3ge6

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    Protein Summary

    The gene Exig_2970 from Exiguobacterium sibiricum 255-15 encodes for a nitroreductase family protein (PF00881).

    It is present as a dimer in the crystal structure and crystal packing analysis suggests that this dimer should be the stable oligomeic form in solution. A Flavin mononucleotide (FMN) molecule is modeled at the putative active site in both protomers.

     dimer_104207.png

     Fig 1. Dimer of 390836 in asu.

     

    During the refinement, the FMN restraints dictionary was modified to allow bending of the isoalloxazine ring along the N5-N10 virtual azis resulting in an improved fit between the FMN coordinates and electron density. The final FMN model is shown in the Figure below.

     

     FMN.png

     

    Fig 2. Final FMN model (atom color, stick) is shown in the omit map (1 sigma). Please notice a slight bending

    along the N5-N10 virtual axis.

     

    Other protein structures that are most similar in structure (by DALI) to this protein are 3bem (putative NAD(P)H nitroreductase YDFN, Z=24.2, 1.9A rmsd, 202 Ca aligned, 29% id, JCSG target), 2b67 (nitroreductase, Z=23.7, 1.9A rmsd, 198 Ca aligned, 28% id, MCSG target). 1nox (NADH oxidase, Z=23.3, 2.0A rmsd, 199 aligned, 28% id), 1nec (nitroreductase, Z=21.8, 2.0A rmsd, 203 Ca aligned, 26% id).

     

    residues.png

    Fig 3.  The residues interacting with the FMN (red) are shown as stick (atomic color). They are Ser18, Arg20, Asn73, Gln76, Gly163, Gly164, Ser199, Arg201. 

     

     

    References

    Hecht, H.J.,  Erdmann, H.,  Park, H.J.,  Sprinzl, M.,  Schmid, R.D. (1995) Crystal structure of NADH oxidase from Thermus thermophilus. Nat.Struct.Biol. 2: 1109-1114
    Abstract ]    View PubMed Abstract at NCBI

    Ligand Summary

     

    A Flavin mononucleotide (FMN) molecule is modeled at the putative active site in both protomers.

    Reviews

    References

     

    No references found.

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    Files (3)

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     dimer_104207.png
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    282.04 kB05:10, 28 Dec 2008gyewonActions
     FMN.png
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    356.41 kB04:09, 20 Feb 2009gyewonActions
     residues.png
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    197.22 kB00:12, 18 Feb 2009gyewonActions
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