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

    Title Crystal structure of a Hypothetical sugar binding protein (BT_4411) from Bacteroides thetaiotaomicron VPI-5482 at 1.25 A resolution. To be published
    Site JCSG
    PDB Id 3see Target Id 393023
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS20938,NP_813322.1, 325003 Molecular Weight 24294.98 Da.
    Residues 221 Isoelectric Point 5.70
    Sequence agvsisaqnliknekfatevtnkvtnpskatagewfimnneadgvttiaweqtgdakypnamkidnsga ekntswykaflgqritdglekgiyvltfyakakeagtpvsvyikqtneekndngklnttffmrrdydad aqpnasgaqynfkikdadkwtkvvvyydmgqvvnaisskksnpalevsdtdddaailkdcyvailgqnk ggvveisdvtlkkk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.25 Rfree 0.1488
    Matthews' coefficent 2.96 Rfactor 0.1298
    Waters 419 Solvent Content 58.46

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3see
    1. Efficient homology search for genomic sequence databases
    M Cameron - 2012 - researchbank.rmit.edu.au
     
    2. Transforming Combustion Research Through Cyberinfrastructure
    Committee on Building Cyberinfrastructure for - 2011 - books.google.com
     

    Protein Summary

    Pfam Summary:

    This did not match anything in the database, so I ran jackhmmer on it and found a few identical proteins from other Bacteroides. However, byt dropping the threshold there was identity to OmpA for the first 100 residues, which may prove helpful. I will not submit a family for this at the moment (might wait until after the next sequence db up-date) as there are too few members, but having the structure will be interesting.

     

    The sequence of Target 393023 has not been classified by the Pfam database.

    Shown below is a ribbons representation of the structure of target id 393023 color coded with the N-terminal end in blue and the C-terminal end in red. However, based on structural similarity with known carbohydrate binding proteins (see table below), target ID 393023 is also likely to be a carbohydrate binding protein.

     

    Update:This did not match anything in the database, so I ran jackhmmer on it and found a few identical proteins from other Bacteroides. However, byt dropping the threshold there was identity to OmpA for the first 100 residues, which may prove helpful. I will not submit a family for this at the moment (might wait until after the next sequence db up-date) as there are too few members, but having the structure will be interesting.


    Update: I have built a family for this now that we have updated the underlying sequence-database> DUF4627 PF15425. In the end there was no obvious relationship with OmpA so the structure will prove very interesting when is comes through. This did not match anything in the database, so I ran jackhmmer on it and found a few identical proteins from other Bacteroides. However, byt dropping the threshold there was identity to OmpA for the first 100 residues, which may prove helpful. I will not submit a family for this at the moment (might wait until after the next sequence db up-date) as there are too few members, but having the structure will be interesting.

    monomer.bmp

     

     

     

    A DALI search of the PDB database shows that target id 393023 shows structural similarity to the following: 

    PDB ID DALI Z-Score rmsd (Ang) length of alignment number of residues in related protein % sequence id

    Description

    1gui 14.5 2.4 147 155 20 CBM4 STRUCTURE AND FUNCTION  [Ref]
    3jxs 14.2 2.3 146 166 15 Crystal structure of XG34, an evolved xyloglucan binding CBM [Ref]
    2zey 12.7 2.8 135 144 18 Family 16 carbohydrate binding module [Ref]
    2xom 12.6 3.0 135 145 15 ATOMIC RESOLUTION STRUCTURE OF TMCBM61 IN COMPLEX WITH BETA-1,4-GALACTOTRIOSE [Ref]
    2oea 12.6 2.8 134 146 19 High-pressure structure of pseudo-WT T4 Lysozyme [Ref]
    2wys 12.5 2.7 139 513 13 HIGH RESOLUTION CRYSTALLOGRAPHIC STRUCTURE OF THE CLOSTRIDIUM THERMOCELLUM N-TERMINAL ENDO-1,4-BETA-D-XYLANASE 10B (XYN10B) CBM22-1-GH10 MODULES COMPLEXED WITH XYLOHEXAOSE [Ref]
    3k4z 12.1 2.9 145 275 14 Crystal Structure of the Cellulosomal CBM4 from Clostridium thermocellum Cellulase CbhA [Ref]

     

    Shown below are the ribbon representations of the superimposed structures of target ID 393023 (blue) and PDB ID 1gui green. Bound carbohydrates from the structure of 1gui are shown by the stick representations. Un-explained difference electron density contoured at 3 sigma above the background level of the map is shown as a pink mesh. This electron density might correspond to one or more unknown ligands bound near the putative active site on target id 393023.  This electron density could not be reliably identified and consisted of two sepate blobs; therefore, it was not modeled.

    1gui_overlap.bmp

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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    Files (2)

    FileSizeDateAttached by 
     1gui_overlap.bmp
    No description
    1420.37 kB02:48, 8 Jun 2011haxelrodActions
     monomer.bmp
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    703.18 kB22:17, 31 May 2011haxelrodActions
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