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The Open Protein Structure Annotation Network
PDB Keyword
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3ff2

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

    Title Crystal structure of uncharacterized cystatin fold protein (YP_497570.1) from NTF2 superfamily (YP_497570.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3ff2 Target Id 391039
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS20870,SARO_25NOV03_CONTIG26_REVISED_GENE949, 3.10.450.50, 325195 Molecular Weight 12810.56 Da.
    Residues 116 Isoelectric Point 4.81
    Sequence lsnletakamiaaynaqdvdtyvsymtddaceanyrgdvvregkegtrsglaaafarwpqnhaeikdaq qvgtyvlmrehvtrgpatdgsplvepfdvvavysfegdkcsrvefir
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.90 Rfree 0.230
    Matthews' coefficent 3.50 Rfactor 0.187
    Waters 200 Solvent Content 64.86

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The Saro_2299 gene encodes for the protein YP_497570 from the SnoaL-like polyketide cyclase family (PF07366). The Conserved Domain Database indicates that it belongs to CD00531(NTF2_like) superfamily. Structural homologs of 3ff2 by Dali are hypothetical proteins and many ketosteroid isomerases (PDB:1qjg and PDB:8cho, etc). The superposition of 3ff2 with 1qjg is shown below. Although they are superimposed well (2.0A rmsd, 109 aligned, 17% id), three major catalytic residues (Tyr14, Asp38 and Asp99) of ketosteroid isomerase are not conserved in 3ff2.

     

     super_1qjg.png

     

    Fig. 1 Superposition of  3ff2 (green) with 1qjg (yellow).

     

    Although 391039 contains a monomer in the crystallographic asymmetric unit, the biomolecule of 3ff2 has been suggested as a dimer according to the calculation of interface interaction(PISA).

     dimer_98022.png

    Fig 1.  Biological molecule of 3ff2

    References:

    Cho, H.S.,  Ha, N.C.,  Choi, G.,  Kim, H.J.,  Lee, D.,  Oh, K.S.,  Kim, K.S.,  Lee, W.,  Choi, K.Y.,  Oh, B.H. (1999) Crystal structure of delta(5)-3-ketosteroid isomerase from Pseudomonas testosteroni in complex with equilenin settles the correct hydrogen bonding scheme for transition state stabilization. J.Biol.Chem. 274: 32863-32868

    Cho, H.S.,  Choi, G.,  Choi, K.Y.,  Oh, B.H.   (1998) Crystal structure and enzyme mechanism of Delta 5-3-ketosteroid isomerase from Pseudomonas testosteroni.  Biochemistry   37: 8325-8330  - 8cho (ligands: p4c)

    Ligand Summary

    An Acetate (ACT) from crystallization condition is found.
     

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    Files (2)

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     dimer_98022.png
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    214.52 kB22:04, 19 Nov 2008gyewonActions
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    178.08 kB03:37, 20 Nov 2008gyewonActions
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