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 A Putative Monooxygenase (YP_001095275.1) from Shewanella loihica PV-4 at 1.26 A resolution. To be published
    Site JCSG
    PDB Id 2ril Target Id 378300
    Molecular Characteristics
    Source Shewanella sp. pv-4
    Alias Ids TPS1723,YP_001095275.1,, 343301 Molecular Weight 11050.00 Da.
    Residues 98 Isoelectric Point 5.45
    Sequence msapvtlinpfkvpadkleaaieyweahrdfmaqqpgylstqlhqsidegatyqlinvaiwqseadfyq aaqkmrqalghvqveglcgnpalyrvirt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.26 Rfree 0.162
    Matthews' coefficent 1.87 Rfactor 0.140
    Waters 110 Solvent Content 34.11

    Ligand Information


    Google Scholar output for 2ril
    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. Quantifying instrument errors in macromolecular X-ray data sets
    K Diederichs - Acta Crystallographica Section D: Biological , 2010 - scripts.iucr.org
    3. Functional consequence of the covalent reaction of phosphoenolpyruvate with UDP-N-acetylglucosamine 1-carboxyvinyltransferase (MurA)
    JY Zhu, Y Yang, H Han, S Betzi, S Olesen - Journal of Biological , 2012 - ASBMB
    4. A chirality_based metrics for free_energy calculations in biomolecular systems
    A Pietropaolo, D Branduardi, M Bonomi - Journal of , 2011 - Wiley Online Library
    5. Applications of Bioinformatics to Protein Structures: How Protein Structure and Bioinformatics Overlap
    GW Han, C Rife, MR Sawaya - Methods in Molecular Biology, 2009 - Springer

    Protein Summary

    This structure is homologous to members of the Dimeric alpha+beta barrel superfamily (d.58.4) from SCOP, including 1lq9, which is a monooxygenase from Streptomyces coelicolor.  Below is a superimposition of this protein with 1lq9.  The gray regions are unaligned.  The aligned regions are colored by weighted variety sequence conservation.  The colors to from red, which is very conserved, to blue, which is not conserved.

    According to Sciara et al., the ligand binding residues in 1lq9 are: Tyr51, Asn62, Trp66, and Tyr72 and "Asn62 and Trp66 are conserved across the monooxygenase family, whereas Tyr51 and Tyr72 are less well conserved, perhaps reflecting the differences in the substrates utilized by the homologous enzymes in the family."  The equivalent residues in this protein are Leu44, Asn58, Trp62, and Phe68.  Below is a close-up of Tyr51 and Asn62 from 1lq9 in green and  Leu44 and Asn58 from this protein in yellow.

    Below is a close-up of Trp66 and Tyr72 from 1lq9 in green and Trp62 and Phe68 from this protein in yellow.

    Ligand Summary





    No references found.

    Tag page

    Files (3)

    FileSizeDateAttached by 
    No description
    104.85 kB22:05, 30 Jun 2008dweekesActions
    No description
    134.44 kB22:05, 30 Jun 2008dweekesActions
    No description
    68.51 kB22:05, 30 Jun 2008dweekesActions
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch