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3rwx

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

    Title Crystal structure of a Hypothetical bacterial outer membrane protein (BF2706) from Bacteroides fragilis NCTC 9343 at 2.40 A resolution. To be published
    Site JCSG
    PDB Id 3rwx Target Id 393211
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS24849,YP_212323.1, 324080 Molecular Weight 27704.34 Da.
    Residues 260 Isoelectric Point 4.70
    Sequence nndddgtnkaqeiagkyegysigncamftdyvmgeksvativpnedgtinvtydsgsgefklnnikvts ktfegsgqvelsmndkpagakdftltgsideqqkltlkvnvpsvmggltiefiqgtlpisyhvsgtynk eanlsvsvgsttypditdckvsikrssddtveltlkglsnlnssqtgramnlgdftvtdvkvtstdnsi fkiegsinttdtnntpitgtlsgtvsnsetnitftfkpgampiditamfkgkk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.40 Rfree 0.2418
    Matthews' coefficent 4.81 Rfactor 0.1984
    Waters 114 Solvent Content 74.42

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Pfam Update: I have built this as Lipocalin_6, and it has 47 members , as PF13944. The other Lipocalins have structures. I have run jackhmmer on it and found 46 homologues, in uncharacterised Bacteroides proteins. Several of these also appear on our new family Lipocalin_4 , PF13648, with high scores, so I would confidently say they would fall into that clan, Calycin (CL0116). There are one or two sturctures solved for Lipocalin_2 for instance, so this is less relevant for us.

     

     

    Target ID 393211 from the human gut-inhabiting bacterium Bacteriodes fragilis belongs to the DUF2897 (PF10988) Pfam family. Residues 137-242 show alignment with this domain. Shown below is a ribbons representation of the structure of target ID 393211 with the N-terminal end in blue and the C-terminal end in red. The structure shows two significant features. First, target ID shows a transmembrane beta-barrel like fold similar to those structure classified in the Omp A-like SUPERFAMILY. Second, the structure determination shows that target id 393211 shows two duplicated domains. Resides 30-146 form an N-terminal domain and residues 150-283 form a C-terminal domain.

     

     

    monomer.png

     

     

     

    Shown below is an overlap of the N-terminal domain (green) (residues 1-146) and C-terminal domains (red) of target id 393211. A pairwise DALI comparisons shows that the N and C terminal domains overlap with an rmsd of 2.4 Angstroms and a sequence identity of 20%

    [Ref]

     

     A search of the PDB using DALI shows that target ID 393211 has similarity to the following structures

     

    PDB ID DALI Z-score rmsd overlap (Angstroms) length of alignment total residues % sequence identity Description
    2f1v  9.4 2.8  111  182  6  Outer  membrane protein Omp W[Ref]
    1jju  8.6 3.8  122  489  6  Structure of a Quinohemoprotein Amine Dehydrogenase with a Unique Redox Cofactor and Highly Unusual Crosslinking[Ref]
    3h3i  8.2 2.8  102  138  15 CRYSTAL STRUCTURE OF A PUTATIVE LIPID BINDING PROTEIN (BT_2261) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.20 A RESOLUTION
    3dzm  8.1 2.8  101  204  4 Crystal structure of a major outer membrane protein from Thermus thermophilus HB27[Ref]
    1p4t 7.9 2.7 100  155  5 Crystal structure of Neisserial surface protein A (NspA) [Ref]

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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