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The Open Protein Structure Annotation Network
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3ecf

    Table of contents
    1. 1. Protein Summary

    Title Crystal structure of NTF2-like Protein (YP_324687.1) from ANABAENA VARIABILIS ATCC 29413 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3ecf Target Id 390455
    Molecular Characteristics
    Source Anabaena variabilis atcc 29413
    Alias Ids TPS14572,YP_324687.1, 3.10.450.50, 88987 Molecular Weight 14875.32 Da.
    Residues 129 Isoelectric Point 5.14
    Sequence matekyheilkkyflsfetgdfsqvqfscnleflspisgntlkgteevipflkgvttrvaevnimsttv eyprasgvwqmrttkgtlytlhnffrldeegivyvwpmfdpkavmenpdaliqwltgkdy
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.90 Rfree 0.222
    Matthews' coefficent 2.14 Rfactor 0.182
    Waters 389 Solvent Content 42.47

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ecf
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     

    Protein Summary

    Gene Ava_4193 from Anabaena variabilis atcc 29413 encodes the YP_324687 protein. It shares weak sequence similarity with the LEH (PF07858) family (FFAS Score: -10.500,Sequence identity: 15%) and the SnoaL (PF07366) family (FFAS score: -13.700, Sequence identity: 13%) from Pfam.  Both of these families are members of the NTF2 (CL0051) clan from Pfam.

    Structurally, 3ecf is similar to members of the NTF2-like superfamily from SCOP. DALI top hits are with several ketosteroid isomerase like PDB:1ogz, PDB:1qjg, PDB:1tuh (Z=14). 3ecf monomer structure is a a+b protein and assumes a barrel fold. The protein's stable oligomeric state is most likely a dimer.

    MG14528A_dimer.png

    Fig 1. Dimer of 3ecf. Each chain has an unidentified density in the core of the barrel. An unknown ligand (UNL) has been modeled into this density based. The UNL bears a strong shape similarity to Benzoate. The figure below shows UNL in the unbiased density (DM map prior to model building).

    UNL.png

     

     

    MG14528A_1u5o.png

    Fig 2. 3ecf (green) is superposed with Nuclear Transport Factor 2 (NTF2) 1oun (cyan), with a rmsd of 2.135 A over an alignment length of 104 amino acids with 9% sequence identity, Dali Zscr=12.

     

    An unknown ligand (UNL) modeled in each monomer resembles benzoate in shape.

    Reviews

    References

     

    No references found.

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