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3ks7

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

    Title Crystal structure of Putative Peptide:N-glycosidase F (PNGase F) (YP_210507.1) from Bacteroides fragilis NCTC 9343 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3ks7 Target Id 393266
    Molecular Characteristics
    Source Bacteroides fragilis nctc 9343
    Alias Ids TPS24867,YP_210507.1, 342458 Molecular Weight 44337.02 Da.
    Residues 396 Isoelectric Point 6.19
    Sequence agghknlpakgdlhipvfenvnvrfspdtypdnyneadgtgvyhlvngriilkkitlpeykrnvsvslk vtlasngdrwdksgscfvlpkssainlltiardgmkfpsvdslklekmvgivpgkdylptvelmrfmtp fgighysnnndslsskrrpvyipkwesnvtwqqditdlypllegeayvgiyidtwtsegylvnadidvk esrlacdvlpkrhveplmntvyymgqsypdifarrdvstdftvpkgaknirlkyivtghgghsggdefv qkrniisvdgkevlnfipwrddcasfrrfnpatgvwlikrlasyigekgytekeveeplassdlsrsnw cpgsdvvpeeavigtlapgkhtftvsipeaqavdgnklnhwlvsaylvwee
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.30 Rfree 0.237
    Matthews' coefficent 2.73 Rfactor 0.201
    Waters 456 Solvent Content 54.88

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ks7

    Protein Summary

    Summary from Pfam: This is probably a two-domain protein, and the N term overlaps with PF09112 and the C-term with PF09113, both of which have structures already.

     

     

     The structure of target ID 393266 has been determined by two-wavelength Se-MAD from an orthorhombic crystal form at a modest resolution of 2.6 Angstroms. The target has been previously classified into two sequence domains in Pfam. Resides 1-140 belong to Pfam B group PB032167; and residues 126-395 belong to PfamB group PB023405. A color-coded ribbons represntation of the monomer is shown below with the N-terminal end of the protein in blue and the C-terminal end in red.

    monomer_view1.png

     A different view of the monomer is shown below.

    monomer_view2.png

     The monomer structure can be described by three subdomains. First there is an N-terminal domain that that forms two beta-sheets (eight strands) in a fold that can be described as that similar to nucleoplasmin-like/viral coat and capsid proteins that forms a beta sandwich (jelly  roll). This N-terminal domain is duplicated in the C-terminal half of the molecule.  The third domain is comprised on two different loops corresponding to residue ranges (162-185) and (328-357). This third domain can be designated as a monomer-monomer interaction domain. Crystal packing suggests that a dimer is a significant oligomerization state in solution. Shown below is a ribbons representation of the dimerdimer.png

     

    A DALI search shows that the  structure of target ID 393266 is significantly similar to three structures (PDB ID 1pnf, 1png, and 1pqs).

     

    PDB ID    Z-Score    rmsd (Ang)    Lalign    Description

    1pnf            26.8        2.7                278      PGNASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE  

    1png           26.7        2.8                277      PEPTIDE-N(4)-(N-ACETYL-D-GLUCOSAMINYL ASPARAGINE AMIDASE

    1pqs           26.6        2.6                278      PGNASE F  FROM FLAVOBACTERIUM MENINGOSEPTICUM

    1phm           7.9         4.8                191      PEPTIDYLHLYCINE ALPHA-HYDROXYLATING MONOXYGENASE (RAT)

    2bbd            7.5         4.6                219      STIV MCP COAT PROTEIN

     

     

     

     

     

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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