.
The Open Protein Structure Annotation Network
PDB Keyword
.

4ezi

    Title Crystal structure of a hypothetical protein (lpg1103) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.15 A resolution. To be published
    Site JCSG
    PDB Id 4ezi 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)
    TPS73930,YP_095136.1
    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 2.14 Rfactor 0.1354
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 42.47

    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 4ezi

    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: a web-site search finds the following insignificant hit: Abhydrolase_6 Alpha/beta hydrolase family Domain CL0028 95 355 107 328 22 198 23.5 4e-05 168 From the E-value the histshould be significant, but as the database has grown so the significant e-value has got smaller, and we rely more on the bit score for setting thresholds. the cut-off is usually around 26-27. Were I to build a family from this seuqence most of the hits would fall into other Abhydrolase families, so it is probably not worth our while. There are many abhydrolases solved already.

     

     

    The x-ray crystal stucture of target ID 418740 was determined at an enhanced resolution of 1.15 Angstroms by Se SAD. A ribbons representation of the structure is shown below:

     

    monomer.png

    A PEG molecule from the crystallization (red stick) was modeled into the putative active site. The program qFit [Ref] was implemented during refinement for the modeling of multiple conformations. The structure indicates that this target belongs to the proline iminopeptidase-like SCOP family, with the overall fold of this protein resembling other alpha/beta hydrolases.

     A DALI structural similarity search reveals some of the many entries in the PDB that show structural similarity to target ID 418740:

    PDB ID Z-score rmsd (Ang) length of alignment number of residues %sequence id Description
    3h2k 46 1.9 356 388 23 Crystal structure of a ligand-bound form of the rice cell wall degrading esterase LipA from Xanthomonas oryzae [Ref]
    2veo 33.5 2.8 328 430 18 X-RAY STRUCTURE OF CANDIDA ANTARCTICA LIPASE A IN ITS CLOSED STATE [Ref]
    3o4h 23.5 2.8 250 577 16 Structure and Catalysis of Acylaminoacyl Peptidase [Ref]
    3azo 22.0 3.1 254 661 10 Crystal structure of puromycin hydrolase [Ref]

     

     

    Shown below is a representation of the putative active site of target id 418740. A molecule of PEG from the crystallization solution was modeled into the putative active site of target id 418740. 2fo-fc electron density (pink) contoured at 1 standard deviation above the background of the map is superimposed on the structure of the bound PEG. Carbon atoms of amino acid residues on target id 418740 are shown in green. The structure of PDB ID 3h2k, a cell wall degrading esterase LipA from Xanthomonas oryzae as well as the top-scoring DALI hit from the PDB, is superimposed on the structure of target id 418740. The carbon atoms of PDB ID 3h2k are shown in cyan. Residues on target ID 418740 are labeled in normal font, and residues on PDB ID 3h2k are labeled in an italic font. Several residues at the active sites are conserved including the catalytic triad Asp 344, His 377, and Ser 195 (target id 418740 numbering). Since PDB ID 3h2k has been implicated in the virulence of Lip A from Xanthomonas oryzae, the structural similarity between target id 418740 and PDB ID 3h2k indicates that target id is involved in a similar function in Legionella pneumophila

     

     

    PEG_actve_site.bmp

    Proline iminopeptidase-like

     

     

     

    Ligand Summary

    Reviews

    References

     

    1. (No Results)

       


      Discuss this publication
    2. (No Results)

       


      Discuss this publication
    3. (No Results)

       


      Discuss this publication
    4. (No Results)

       


      Discuss this publication
    5. (No Results)

       


      Discuss this publication
    Tag page
    • No tags

    Files (2)

    FileSizeDateAttached by 
     monomer.png
    No description
    258.53 kB16:22, 2 Apr 2012haxelrodActions
     PEG_actve_site.bmp
    No description
    968.02 kB19:56, 2 Apr 2012haxelrodActions
    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