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3scy

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

    Title Crystal structure of a Hypothetical bacterial 6-phosphogluconolactonase (BF1038) from Bacteroides fragilis NCTC 9343 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 3scy Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS64795,YP_210724.1, 88020
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 1.95 Rfactor 0.1641
    Waters
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    Solvent Content 36.76

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3scy

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    Protein Summary

    Target 390120 has a 7-bladed beta-propeller fold. It has been crystallized as a dimer, but in fig GS13263B.png  (see below) only one monomer is shown.

    Sequence analysis: FFAS, against Pfam, top hit 3-carboxy-cis,cis-muconate lactonizing enzyme (score -85.100, PF10282.2, Q2B585_9BACI/7-347). Blast, against SwissProt, all significant hits with assingned funtion were with 6-phosphogluconolactonase.

    Structural analysis: Dali 3rd hit (1st hit with assigned function) with PUTATIVE ISOMERASE YBHE (1ri6, Z-score 32.9) - classified as E.C.3.1.1.31 by Enzyme Structures Database (http://www.ebi.ac.uk/thornton-srv/databases/enzymes/).

    Note that the Pfam Lactonase family (PF10282) contains bacterial 6-phosphogluconolactonases (6PGL)YbhE-type ( EC:3.1.1.31) and  fungal muconate lactonising enzyme carboxy-cis,cis-muconate cyclase ( EC:5.5.1.5) and muconate cycloisomerase ( EC:5.5.1.1). For the reasons detailed above and considering the fact that this target is bacterial, it might be considered as an hypothetical bacterial 6-phosphogluconolactonase.

    The structure of target id 390120 was determined by Se-MAD phasing at a resolution of 1.50 Ang. Shown below are two views of the structure of target id 390120. An unknown ligand represented by red cylinders with superimposed electron density (grey, contoured at 1 sigma above the background level of the map) is also shown. The second view below is looking along the axis of the beta-propeller.

    view1.bmp

     

    view2.bmp

     

     

     

    A DALI search of the PDB shows that target ID 390120 shows similarity to the following structures

    PDB ID DALI Z-score rmsd overlap length of alignment total residues % sequence identity Description
    3fgb 62.3 0.5 349 349 75 Crystal structure of the Q89ZH8_BACTN protein from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR289b.
    3hfq 47.0 1.7 332 341 32 Crystal structure of the lp_2219 protein from Lactobacillus plantarum. Northeast Structural Genomics Consortium Target LpR118
    1ri6 45.2 1.5 319 333 25 Structure of a putative isomerase from E. coli
                 
                 
                 
                 
                 
                 
                 

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

    FileSizeDateAttached by 
     GS13263B.png
    No description
    235.82 kB21:31, 13 May 2011marianaActions
     view1.bmp
    No description
    1420.37 kB16:43, 7 Jun 2011haxelrodActions
     view2.bmp
    No description
    1420.37 kB16:43, 7 Jun 2011haxelrodActions
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