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3o14

    Title Crystal structure of an anti-ECFsigma factor, ChrR (Maqu_0586) from Marinobacter aquaeolei VT8 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3o14 Target Id 403193
    Molecular Characteristics
    Source Marinobacter aquaeolei vt8
    Alias Ids TPS30648,YP_957874.1, 2.60.120.10, 324441 Molecular Weight 24320.96 Da.
    Residues 222 Isoelectric Point 5.03
    Sequence meinadftkpvvidtdqlewrpspmkgverrmldriggevaratsivryapgsrfsahthdggeefivl dgvfqdehgdypagtyvrnppttshvpgsaegctifvklwqfdpadrtqfsknmeaelgapvegistsl lhederetvthrklepganltseaaggievlvldgdvtvndevlgrnawlrlpegealsatagargaki wmktghlrfvrtpev
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.1872
    Matthews' coefficent 2.27 Rfactor 0.1522
    Waters 568 Solvent Content 45.74

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3o14
    1. Assessment of ligand_binding residue predictions in CASP9
    T Schmidt, J Haas, TG Cassarino - Structure, Function, and , 2011 - Wiley Online Library
     
    2. FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins
    D Roche, S Tetchner, L McGuffin - BMC bioinformatics, 2011 - biomedcentral.com
     
    3. Blind prediction of quaternary structures of homo-oligomeric proteins from amino acid sequences based on templates
    M Morita, M Kakuta, K Shimizu, S Nakamura - 2012 - hoajonline.com
     

    Protein Summary

     The protein YP_957874.1 is annotated as anti-ECFsigma factor, ChrR.

    A sequence search at PFAM suggests that this protein belongs to the Cupin domain family PFAM:PF07883.

    Note from PFAM: added this as a new family in Pfam (Cupin_7 PF12973) and this family has been added to the Cupin clan.

    The protein has two barrel domains. A Zn ion is bound to one of the domains as shown below.

    MJ9145D.png

     

    The two domains, when split at residue 123, can be superimposed on each other with a rmsd of 1.82 Angstrom over 85 residues . However, the metal binding site is not conserved.

    The details of interaction of protein with Zn are shown below.

    MJ9145D_Zn.png

     

     

     There are a few structurally similar proteins available in PDB.

    DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 PDB:1sfn 20.8 2.5 200 245 13 Conserved Hypothetical Protein
    2 PDB:2qdr 20.7 2.6 206 285 15 Uncharacterized Protein
    3 PDB:1sef 19.5 2.7 203 250 13 Conserved Hypothetical Protein
    4 PDB:1rc6 19.2 2.5 195 242 11 Hypothetical Protein Ylba
    5 PDB:1tq5 19.0 2.9 192 234 13 Protein Yhhw
    6 PDB:2p17 18.8 2.8 194 249 13 Pirin-like Protein
    7 PDB:1y3t 18.2 2.4 198 330 13 Hypothetical Protein Yxag
    8 PDB:2h0v 18.1 2.4 198 335 13 Quercetin 2,3-dioxygenase
    9 PDB:1sq4 18.1 2.7 201 270 13 Glyoxylate-induced Protein
    10 PDB:1gqh 18.0 2.6 197 333 14 Quercetin 2,3-dioxygenase

     

    A superposition of this protein (green) with PDB:1sfn (magenta) shows the similarity between the two structures. There is no metal bound to 1sfn and the metal binding site is not fully conserved (only one His instead of the three His residues).

    MJ9145D_1sfn.png

    Ligand Summary

    Reviews

    References

     

    No references found.

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