The Open Protein Structure Annotation Network
PDB Keyword


    Title Crystal structure of uncharacterized protein conserved in bacteria with a cystatin-like fold (YP_168589.1) from SILICIBACTER POMEROYI DSS-3 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3flj Target Id 391435
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS24316,YP_168589.1, 3.10.450.50, 336132 Molecular Weight 15394.02 Da.
    Residues 136 Isoelectric Point 5.91
    Sequence mhptiarmqevvakgdeslihallaedvrfmpptyyktwtgrdpvaavlghvgqvfsefryrrimgegk dwalefqckvgeldavgvdlitlneggliqdfevvmrpyktvgalrdamnarvmtdarflkyreals
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.00 Rfree 0.185
    Matthews' coefficent 4.07 Rfactor 0.176
    Waters 105 Solvent Content 69.74

    Ligand Information


    Google Scholar output for 3flj
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org

    Protein Summary

    YP_168589.1 is annotated as a hypothetical protein. A sequence analysis does not suggest any PFAM family.


    Note from PFAM:

    It was found to overlap  with Snoal_2 PF12680 and NTF2 PF02136.


    The monomer structure is alpha+beta structure shown below.



    The protein assembles as a dimer in crystal structure and this dimer may likely be its solution state too.


    There is some unidentified density in the core of the protein surrounded by both hydrophobic and hydrophillic residues. This density has been modeled with an unknown ligand (UNL), shown below in spehrical representation. The density around the protein and UNL are unbiased density obtained after phasing and density modification and is contoured at one sigmaa above the mean.



    Although the function of this protein is unknown, the structural homologs suggest this protein to be a steroid delta isomerase.  Top ten DALI hits are shown in the table below.

    DALI Structural Homologs
    1 1w02 12.8 2.4 110 119 18 STEROID DELTA-ISOMERASE
    2 1tuh 12.8 2.5 117 131 15 HYPOTHETICAL PROTEIN EGC068
    3 1ohp 12.6 2.4 111 125 14 STEROID DELTA-ISOMERASE
    4 1oh0 12.6 2.4 111 125 19 STEROID DELTA-ISOMERASE
    5 2pzv 12.5 2.4 109 123 19 STEROID DELTA-ISOMERASE
    6 2inx 12.5 2.4 109 123 19 STEROID DELTA-ISOMERASE
    7 2b32 12.5 2.5 110 123 19 STEROID DELTA-ISOMERASE
    8 1w6y 12.5 2.5 112 125 19 STEROID DELTA-ISOMERASE
    9 1vzz 12.5 2.4 110 123 18 STEROID DELTA-ISOMERASE
    10 1ogx 12.5 2.5 111 126 19 STEROID DELTA-ISOMERASE


    Some of these structures are shown below superimposed on this protein.


    Color scheme: YP_168589.1 (green), 1oh0 (cyan), 1tuh (lightmagenta), 3en8 (yellow)

    Another very similar JCSG structure, not identified in DALI search is 3f8x, which is a putative Delta-5-3-ketosteroid Isomerase.




    No references found.

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