The Open Protein Structure Annotation Network
PDB Keyword


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

    Title Crystal structure of Uncharacterized peroxidase-related protein (YP_604910.1) from Deinococcus geothermalis DSM 11300 at 1.51 A resolution. To be published
    Site JCSG
    PDB Id 2oyo Target Id 371529
    Molecular Characteristics
    Source Deinococcus geothermalis dsm 11300
    Alias Ids TPS1583,YP_604910.1, 104237 Molecular Weight 21690.49 Da.
    Residues 195 Isoelectric Point 5.60
    Sequence mtttqpeakdrisslpvpdatqvpegvrklwakaeanigfvpnvfraqavngeqflawwnyfnlllnke gyltnaerelvavvvsgvnrclycavshgaalreflgdpqkadavavnwrhadltereqalaayaeklt rhpaevtaadleplravglddhqimelvqvigmfnltnrvssalgfvpnpeyyrqar
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.51 Rfree 0.215
    Matthews' coefficent 2.38 Rfactor 0.182
    Waters 441 Solvent Content 48.41

    Ligand Information


    Google Scholar output for 2oyo
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
    2. MrGrid: a portable grid based molecular replacement pipeline
    JW Schmidberger, MA Bate, CF Reboul - PloS one, 2010 - dx.plos.org
    3. Crystal structure of alkyl hydroperoxidase D like protein PA0269 from Pseudomonas aeruginosa: Homology of the AhpD-like structural family
    T Clarke, V Romanov, Y Chirgadze - BMC structural , 2011 - biomedcentral.com

    Protein Summary

    The Dgeo_1446 gene encodes the YP_604910.1 amino acid sequence which folds into a single domain 195 residues long protein showing the signature of the Carboxy-Mucono-lactone Decarboxylase (CMD) group from positions 50 to 135 with a highly conserved C90-C93-H97 motif (PF02627). Based on the genome context where its gene is located, STRING gives a 0.65 score to the possible functional partner PF04306, a putative membrane protein. 


    SCOP classifies 2oyo as belonging to the all alpha class, AhpD-like superfamily, Atu0492-like family. FFAS and HHpred provide the closely related 2pfx as top hit, followed by 2prr and 3c1l, all uncharacterized peroxidase-related proteins. FATCAT and Dali corroborate hits. The secondary structure matching server gives a 91% and 82% score to 2prr and 3c1l, respectively.

    Ligand Summary





    No references found.

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