The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of TETR family transcriptional regulator (YP_001095692.1) from SHEWANELLA SP. PV-4 at 2.05 A resolution. To be published
    Site JCSG
    PDB Id 3gzi Target Id 379941
    Molecular Characteristics
    Source Shewanella sp. pv-4
    Alias Ids TPS24225,YP_001095692.1, _0009.003259_, 87068 Molecular Weight 24867.36 Da.
    Residues 217 Isoelectric Point 6.54
    Sequence maeaksrvgrpsgdtqnrdklilaarnlfierpyaqvsireiaslagtdpgliryyfgskeklfstmih etampvlaqlhkarretrqespaallqtyysvmskhphfprlmlriagldqslpenaevtkafyevvnf eniaifqrlkdknllkddvdahcaqlsffammvfpfivpenllervgieltpdflqllaeqntrllqrg lmdvkderde
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.05 Rfree 0.248
    Matthews' coefficent 2.42 Rfactor 0.187
    Waters 128 Solvent Content 49.14

    Ligand Information



    Protein Summary

    Gene Shew_3567 from Shewanella sp. pv-4 encodes the YP_001095692 protein that shows sequence similarity to the bacterial regulatory proteins of the tetR family (PF00440). Its genome context suggests a functional link (score 0.87) with neighboring genes Shew_3566, an efflux transporter of the RND family, and Shew_3565, an accriflavin resistance protein.

    Pre-SCOP classifies 3gzi N-terminal domain (7-82) in the all alpha class, homeodomain-like superfamily, tetracyclin repressor-like N-terminal domain family; the C-terminal domain (93-212) in the tetracyclin repressor-like C-terminal domain (super)family. A DALI search results in many hits with transcriptional regulators of the TerR family like 3dew (Z=15), 1t33 (Z=14), 1bhq, 2d6y (Z=13) and 2id6 (Z=12). A superposition of 3gzi with the DALI best hit (3dew) is shown below. The 3gzi structure contains one monomer in assymetric unit. However, crystal packing analysis by PISA suggests that a dimer could be the stable oligomeic form in solution. During refinement, an unidentified ligand (UNL, red spheres) was modeled in the putative binding site.



    Fig 1. Monomer of 3gzi                                              Fig 2. The biological dimer of 3gzi




    Fig 3. Superposition of 3gzi (green) and 3dew (yellow).



    Fig 4. Superposition of 3gzi (light blue) and TerR (PDB: 2trt, light yellow). UNL (red dots) of 3gzi is shown with the omit map (1 sigma, blue). The UNL is located in the tetracyclin (TAC, orange stick) binding site of the TerR protein (rmsd=3.5A, seq id=10%).

    Ligand Summary


    An Unidentified ligand (UNL) in the putative ligand binding site is modeled.

    Ethylene glycol (EDO) molecules are modeled.




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