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

    Title Crystal structure of a Putative aromatic-ring hydroxylating dioxygenase (TM1040_3219) from SILICIBACTER SP. TM1040 at 1.80 A resolution. To be published
    Site JCSG
    PDB Id 3n0q Target Id 397279
    Molecular Characteristics
    Source Silicibacter sp. tm1040
    Alias Ids TPS29608,YP_611455.1, _0018.000681_, _0004.000710_, 324842 Molecular Weight 46088.31 Da.
    Residues 408 Isoelectric Point 5.72
    Sequence mhsnintlianhraghaldqafytdaevfqtdlqeifykewlfaipaceldkpgsyvthqvgnynviiv rgadnvirafhnacrhrgsvickakkgnnpklvcpyhqwtyeldgrllwardmgpdfepsrhglktvhc relagliyicladeapdferfaevarpylevhdlsnakvahessivergnwklvwennrecyhcggnhp alcrtfpddpsvtgieggetpsnlqahfdrceqagmpsgfhlsgdgqfrvarmplkegaesytmdgkta vrrwlgraafadagsllkfhypttwnhflsdhsivfrvtpisptetevttkwlvhkdavegvdydlqrl tevwiatndedrevvefnqmginspayepgpysptqesgvlqfvewylstlkrnsgphavaae
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.80 Rfree 0.186
    Matthews' coefficent 2.85 Rfactor 0.154
    Waters 479 Solvent Content 56.85

    Ligand Information


    Google Scholar output for 3n0q
    1. Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase
    KD Daughtry, Y Xiao, D Stoner-Ma, E Cho - Journal of the , 2012 - ACS Publications
    2. Phylogenetic analysis reveals the surprising diversity of an oxygenase class
    JK Capyk, LD Eltis - Journal of Biological Inorganic Chemistry, 2011 - Springer

    Protein Summary

    This protein is annotated as a Rieske (2Fe-2S) domain protein belonging to Pfam PF00355

    It is present as a monomer in the asymmetric unit of the crystal structure, but crystal packing analysis predicts that the solution state form should be a trimer.

    Calculation of Anomalous Difference Fourier (ADP) electron density maps from x-ray data collected above and below the excitation energies for Fe and Ni confirm the presence of the 2Fe-2S cluster as well as Ni at sites away from the cluster.

    The 2Fe-2S cluster is formed by coordination with conserved residues Cys83, Cys103, His85 and His106.

    One of the Ni binding sites involved the interaction of Ni with His201, His206, Asp356 and a Tris molecule. The second Ni site involves coordination with the surface residue His16 and another Tris molecule and is involved in interaction with a symmetry-related molecule. The Ni and Tris are present in the crystallization solution.


    Information on other similar proteins can be found from the links above to Pfam and FFAS.

    A search for the proteins with the most closely related structure to this one using the EBI SSM server result in more than 20 hits with Q-scores > 0.30. Some of their PDB accession ids are 2ckf, 3eqq, 3en1, 1ndo, etc. which are mainly napthalene, toluene and biphenyl dioxygenases.

    Based on this, it is likely that this protein may be involved in the hydroxylation and subsequent degradation of aromatic compounds.

    Ligand Summary

    FES: [2Fe-2S] cluster

    NI: Nickel

    TRS: Tris




    No references found.

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