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The Open Protein Structure Annotation Network
PDB Keyword
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3eby

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

    Title Crystal structure of the beta subunit of a putative aromatic-ring-hydroxylating dioxygenase (YP_001165631.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.75 A resolution. To be published
    Site JCSG
    PDB Id 3eby Target Id 391042
    Molecular Characteristics
    Source Novosphingobium aromaticivorans dsm 12444
    Alias Ids TPS18315,YP_001165631.1, 3.10.450.50, 85619 Molecular Weight 17897.27 Da.
    Residues 162 Isoelectric Point 4.84
    Sequence msvaaevaqvaqsaiddfnaayglcldddrleqwptlfvddclyqviarenvdnglpaavmycdskgml adrvvalrkanvfpehfnrhligravitgvegdqvsaeasyvvfqtrndgetriynagkyvdrfdlsgg tvrlksrtciydtlriatllatpi
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.75 Rfree 0.205
    Matthews' coefficent 2.48 Rfactor 0.168
    Waters 175 Solvent Content 50.46

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3eby
    1. Modeling discrete heterogeneity in X-ray diffraction data by fitting multi-conformers
    H Van Den Bedem, A Dhanik, JC Latombe - Section D: Biological , 2009 - scripts.iucr.org
     
    2. Dimensionality reduction in computational demarcation of protein tertiary structures
    RR Joshi, PR Panigrahi, RN Patil - Journal of Molecular Modeling, 2011 - Springer
     

    Protein Summary

     MG11732J /YP_001165631.1 is a protein with 162  residues from Sphingomonas aromaticivorans.  The search results from NCBI sequence alignment reveals that this target may be a Small subunit aromatic oxygenase belong to the NTF2 superfamily. This protein should be a structural homolog to structure 2CKF, 2GBW, 2B1X and 1WQL.There is one YP_001165631.1 molecule in each asymmetric unit.  The interface interaction suggests that the biomolecule of NP_940074.1  be a trimer.

       


    391042_1.png

    Figure 1. Protein YP_001165631.1  belongs to the NTF-2 super family with an α/β-barrel fold.  

       

    391042_2.png

       

    Figure 2. The biomolecule of YP_001165631.1 is a dimer based on interface interaction.

       

    391042_3.png

      Figure 3. Protein YP_001165631.1 (green) is structural homolog to 2CKF, 2GBW, 2B1W and 1WQL.  


       

       

       

       

       

       

       

       

       

       

       

       

       

       

       

       

    1.    Gakhar, L.,  Malik, Z.A.,  Allen, C.C.,  Lipscomb, D.A.,  Larkin, M.J.,  Ramaswamy, S.  (2005) Structure and Increased Thermostability of Rhodococcus sp. Naphthalene 1,2-Dioxygenase.  J.Bacteriol.  187: 7222-7231(PDB ID 2B1X)


    2.    Ferraro, D.J.,  Brown, E.N.,  Yu, C.L.,  Parales, R.E.,  Gibson, D.T.,  Ramaswamy, S.  (2007) Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.  Bmc Struct.Biol.   7: 10-10   (PDB ID: 2GBW)

    3.    Jakoncic, J.,  Jouanneau, Y.,  Meyer, C.,  Stojanoff, V.   (2007) The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1.  Biochem.Biophys.Res.Commun.   352: 861-866   (PDB ID: 2CKF)

    4.    Dong, X.,  Fushinobu, S.,  Fukuda, E.,  Terada, T.,  Nakamura, S.,  Shimizu, K.,  Nojiri, H.,  Omori, T.,  Shoun, H.,  Wakagi, T.  (2005) Crystal Structure of the Terminal Oxygenase Component of Cumene Dioxygenase from Pseudomonas fluorescens IP01  J.BACTERIOL.  187: 2483-2490   (PDB ID: 1WQL)

    Ligand Summary

    Reviews

    References

     

    No references found.

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