.
The Open Protein Structure Annotation Network
PDB Keyword
.

3iee

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

    Title Crystal structure of hypothetical protein BF3319 from Bacteroides fragilis (YP_212931.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3iee Target Id 393163
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS26577,YP_212931.1, 324032 Molecular Weight 30212.04 Da.
    Residues 269 Isoelectric Point 8.31
    Sequence ascsggdkskapvvstadienaaevikyyntslgvlkdmvkekdvnavldymeqkgktpalsaivppav vskdsaivlnpgncfneetrrnlkqnytglfqartefyanfdtylsylkkkdvtnakklldvnyqlstq mseykqnifdilspfteqaelvllvdnplkaqimsvrkmsstmqsilnlyarkhrmdgpridlkvaelt kqldaakklpvvnghegemksyqaflsqvetfikqvkkvrekgeysdadydmltsafetsii
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.70 Rfree 0.192
    Matthews' coefficent 2.17 Rfactor 0.164
    Waters 344 Solvent Content 43.44

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3iee

    Protein Summary

    Pfam update: I have built this as a small family which may bear similarity to the one indicated:
    ID DUF3829
    AC PF12889
    DE Protein of unknown function (DUF3829)
    AU Coggill P
    SE JCSG_target_393163_3iee
    GA 21.30 21.30;
    TC 21.30 21.30;
    NC 21.10 21.00;
    BM hmmbuild --amino -o /dev/null HMM SEED
    SM hmmsearch -Z 9421015 -E 1000 --cpu 4 HMM pfamseq
    TP Family This is a small family of proteins from several bacterial species, whose function is not known. It may, however, be related to the GvpL_GvpF family of proteins, Pfam:PF06386.

    Gene BF3319 from Bacteroides fragilis nctc 9343 encodes an all alpha-helical protein, that shows no Pfam hit.
    The protein structure, 3iee, contains a monomer in the crystallographic asymmetric unit, which is also a biological unit.

    A.png


    Fig.1. 3iee structure.

     Dali hits ligand binding domain of aspartate receptor (2asr, Z=9.7, rmsd=2.4A, 100 Ca aligned, 7% id), apolipoprotein E (1ya9, Z=9.5, rmsd=2.9A, 101 Ca aligned, 7% id) and acethylcholine receptor protein, alpha chain (1oed, Z=9.4, rmsd=2.7A, 101 Ca aligned, 7% id). As shown below, N-terminal of 3iee (green) is similar to 2asr (cyan), and C-terminal of 3iee (green) is similar to 1ya9 (light blue) and 1oed (light pink).

     

    Nterminal.png

    Fig. 2. 2asr (cyan) superimposes to the N-terminal domian of the 3iee (green) only.

    C-terminal.png

    Fig. 3. 1ya9 (light blue) and 1oed (light pink) superimpose to the C-terminal domain of the 3iee (green).

     

    References

    Bowie, J.U.,  Pakula, A.A.,  Simon, M.I. (1995) The three-dimensional structure of the aspartate receptor from Escherichia coli. Acta Crystallogr.,Sect.D 51: 145-154
      View PubMed Abstract at NCBI   ACTALink out to ACTA Abstract for: 2ASR

     

    Hatters, D.M.,  Peters-Libeu, C.A.,  Weisgraber, K.H. (2005) Engineering conformational destabilization into mouse apolipoprotein E. A model for a unique property of human apolipoprotein E4 J.Biol.Chem. 280: 26477-26482
       View PubMed Abstract at NCBI

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags

    Files (3)

    FileSizeDateAttached by 
     A.png
    No description
    183.03 kB07:34, 23 May 2009gyewonActions
     C-terminal.png
    No description
    159.54 kB07:43, 23 May 2009gyewonActions
     Nterminal.png
    No description
    179.49 kB07:43, 23 May 2009gyewonActions
    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