.
The Open Protein Structure Annotation Network
PDB Keyword
.

3hoi

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

    Title Crystal structure of FMN-dependent nitroreductase BF3017 from Bacteroides fragilis NCTC 9343 (YP_212631.1) from Bacteroides fragilis NCTC 9343 at 1.55 A resolution. To be published
    Site JCSG
    PDB Id 3hoi Target Id
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS25947,YP_212631.1, 3.40.109.10, 326302
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 1
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.39 Rfactor 0.161
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 48.44

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
    parameter 'target' could not convert from 'list' to 'str' (click for details)
    Google Scholar output for 3hoi

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    Pfam update: This protein is now in family PF00881.17 Nitroreductase along with other structures.

    Gene YP_212631.1 encodes a protein with 211 residues from Bacteroides fragilis nctc 9343. It has been annotated as a putative exported protein belonging to Nitroreductase Pfam family PF00881. Several JCSG targets including2r01, topsan_page, 3ek3, topsan_page, 3eof, topsan_page and 3gfa, topsan_page  belong to this family.

    The YP_212631.1 is present as a monomer in the asymmetric unit of the unit cell of the crystal structure (Fig. 1), and packing analysis suggests that the dimer with symmetry mate (cyan and light blue) is the relevant oligomeric form in solution. In the putative active site of the protein, a Cl ion  and a FMN (red sticks) are found. 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. During QC round, Cl ion was replaced to UNL.

     monomer.png

    Fig.1. Crystal structure of YP_212631.1 in the asymmetric unit.

    dimer.png

    Fig. 2. Biomolecule of YP_212631.1.

     

    UNL.png

    Fig. 3. The surface representation of the YP_212621.1 shown putative active site. Final FMN (red stick) and UNL (balls) in the EDs (grey mesh) are shown. Although it didn't refine well, the EDs resemble either disordered Cl or acetate ions.

     

    References

    Kobori T, Sasaki H, Lee WC, Zenno S, Saigo K, Murphy ME, Tanokura M.Structure and site-directed mutagenesis of a flavoprotein from Escherichia coli that reduces nitrocompounds: alteration of pyridine nucleotide binding by a single amino acid substitution. J Biol Chem. 2001 Jan 26;276(4):2816-23. Epub 2000 Oct 16.

    Ligand Summary

     

    Unknown ligand (UNL), sulfate ions (SO4), citrate anion (FLC) and PEG fragement (PEG) were found.

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch