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 hypothetical protein MJ_1460 (1592102) from Methanococcus jannaschii at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 2osd Target Id 373077
    Related PDB Ids 2oso 
    Molecular Characteristics
    Source Methanocaldococcus jannaschii dsm 2661
    Alias Ids TPS1617,1592102, BIG_84, PF02830 Molecular Weight 18782.10 Da.
    Residues 162 Isoelectric Point 5.07
    Sequence mafmekifpdileairneeiikeskkipmpyfglfalvifdkvkelgsetslyeigeefgkmlspknie elkkifklmnfgdleidenkillknppykiklsnppyqwvskeepihdfiagilagcleeifkkkfvvn evecvsqgkdkcvfevkevdelnk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.30 Rfree 0.242
    Matthews' coefficent 2.41 Rfactor 0.219
    Waters 30 Solvent Content 48.95

    Ligand Information


    Google Scholar output for 2osd
    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. Three Dimensional Model for N-Terminal A Domain of DmpR (2-Dimethylphenol) Protein Based on Secondary Structure Prediction and Fold Recognition
    PS Suresh, R Kumar, A Kumar - In Silico Biology, 2010 - IOS Press

    Protein Summary

    The gene MJ_1460 translates into the NP_248464 protein containing a ~60 residues long V4R (vinyl-4-reductase) domain at its C-terminus (PF02830). So far, 185 proteins, all from prokaryotes, share the same domain architecture. Its HMM profile shows high conservation of a sequence motif C/H-E-C-C. The equivalent residues in 2osd (H116-E139-C142-C150) chelate a Zn ion in the crystal structure.

    SCOP classifies 2osd as belonging to the alpha+beta class, superfamily of "ligand binding in the NO signaling and Golgi transport", MJ1460-like family. In agreement, a subunit of the ER-Golgi protein traffiking complex 2j3w is a relevant hit coming from HHpred (P-val=1.3e-6), FATCAT (P-val=1.15e-4), Dali (Z-scr=10.5) and FFAS (score -10.3); and 2o09 , a Heme-NO binding domain, is selected by both SSM (75% SSE) and FFAS (score -11.4) (Dali Z=7). A different H-NOX structure, 1u55, is detected by fastSCOP (e-val=2e-8) and FATCAT (P-val=2.25e-5) (Dali Z=6).

    Ligand Summary





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