.
The Open Protein Structure Annotation Network
PDB Keyword
.

3cjx

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

    Title Crystal structure of protein with a cupin-like fold and unknown function (YP_298765.1) from Ralstonia eutropha JMP134 at 2.60 A resolution. To be published
    Site JCSG
    PDB Id 3cjx 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)
    TPS1755,YP_298765.1, 2.60.120.10
    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 2.54 Rfactor 0.203
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 51.60

    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 3cjx

    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

    The Reut_B4571 gene from Ralstonia eutropha jmp134 encodes the YP_298765 protein that could belong (very weak e-val=0.006) to the cupin2 family (PF07883). The genomic neighborhood of the homologous protein from Shewanella sp. shows a potential functional link of this target with an alcohol dehydrogenase (score 0.8).

    Pre-SCOP classifies 3cjx in the all beta class, RmlC-like cupins superfamily, TM1287-like family. The 3cjx structure folds into a 10 anti-parallel beta-strands and an alpha-helix at the C-terminal end of the chain. The beta-strands are arranged to form two five stranded anti-parallel beta-sheets. The two individual beta-sheets, in turn, are twisted to form a jellyroll beta-sandwich with a topology characteristic of a cupin barrel-fold. In solution and in the crystal, a tetramer most likely represents the biologically significant oligomerization state. Pairs of monomers (figure1 blue:green and yellow:red) are tighly packed across the beta-barrel interface. However, additional inter-subunit contacts form in the tetramer with the N-terminal region of one subunit forming a two stranded anti-parallel beta-sheet with the C-terminal beta strand of a second subunit.


    DALI returns as top hit the uncharacterized cupin 3ebr (Z=20), followed by the putative alpha carboxylase 2o1q (Z=17) and the acetylacetone cleaving enzyme 3bal (Z=16). From a search of the EBI Secondary Fold Matching Server (EBI SSM server) using the refined coordinates of 3cjx as query shows as top hit the PDB ID 1LRH (Z=12). 1RLH is an auxin binding protein from the maize plant. Even though the two structures show only a 15% sequence identity, there is only a 1.9 Angstrom RMS between their 129 aligned Ca atoms.


    Figure 1. Ribbon representation of the 3cjx crystal structure. The biologically relevant oligomerization state is believed to be a tetramer. Each monomer within the tetramer is rendered in a unique color.

     

     

     

     

    Ligand Summary

    Glycerol molecules from the cryoprotectant and chloride molecules from the crystallization buffer were modeled into the 3cjx structure.

    References

    Reviews

    References

     

    No references found.

    Tag page
    • No tags

    Files (1)

    FileSizeDateAttached by 
    FG7408A.png
    No description
    158.75 kB22:05, 30 Jun 2008dweekesActions
    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