.
The Open Protein Structure Annotation Network
PDB Keyword
.

3kez

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

    Title Crystal structure of Putative sugar binding protein (YP_001299726.1) from Bacteroides vulgatus ATCC 8482 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3kez 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)
    TPS26688,YP_001299726.1, BIG_773, 332835
    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 2
    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 2.25 Rfactor 0.152
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 45.39

    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 3kez
    1. Quantifying instrument errors in macromolecular X-ray data sets
    K Diederichs - Acta Crystallographica Section D: Biological , 2010 - scripts.iucr.org
     

    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

    This protein is annotated as a putative outer membrane protein possibly involved in nutrient binding and belongs to the Pfam family of SusD_RagB proteins (Pfam update:This protein is now in family PF07980.4 SusD CL0020),

    PF07980

    .

    It is similar in structure to several other putative SusD structures solved at the JCSG. They can be found through the FFAS link above and a nice description of these structures as well as other similar structures can be found on the Topsan page for PDB id 3hdx.

    There are 2 molecules in the asymmetric unit in the crystal structure, but crystal packing analysis and analytical size-exclusion chromatography support the assignment of a monomer as the significant oligomerization state in solution.

    Fig1revised.png

    An endogenous Ca2+ ion (pink sphere, above) has been tentatively modeled into the crystal structure near residue 346 in both chains that interacts with Gln343, Glu346, Asn352 and the carbonyl oxygen of Asp350 (all in pink, below) . Calcium ions satisfy the electron density (and have an appropriate B-factor after refinement) better than water molecules or Na+ ions and have suitable coordination geometry. A similar endogenous calcium binding site has also been observed in the crystal structure of another SusD protein with PDB id 3ck7 (orange, below). However, it is not believed to have any functional significance, as yet.

    Fig2.png

    Ligand Summary

    Ca2+ ions (endogenous) have been tentatively modeled. See above for details.

    Reviews

    References

     

    No references found.

    Tag page
    • No tags

    Files (2)

    FileSizeDateAttached by 
     Fig1revised.png
    No description
    465.63 kB21:37, 23 Oct 2009debanuActions
     Fig2.png
    No description
    769.11 kB22:05, 23 Oct 2009debanuActions
    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