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PDB Keyword
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3es1

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

    Title Crystal structure of protein with a cupin-like fold and unknown function (YP_001165807.1) from NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 at 1.91 A resolution. To be published
    Site JCSG
    PDB Id 3es1 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS14629,YP_001165807.1, 2.60.120.10, 85592
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 2.51 Rfactor 0.170
    Waters
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    Solvent Content 50.94

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3es1

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    Protein Summary

    Gene Saro_3421 from Novosphingobium Aromaticivorans DSM 12444 encodes the YP_001165807.1 protein.  The search results from NCBI sequence alignment reveals that this target belong to the CUPIN-2 superfamily (PF07883). Genome context analysis provides two 0.9 scored hits, based on neighborhood and co-ocucrrence, with the genes Saro_3422 (fumarylacetoacetate hydrolase) and with Saro_3435 (NAD-dependent epimerase/dehydratase).    

     

    SCOP classifies 3es1 in the all beta class, RmlC-like cupins superfamily. DALI hits are with the Mn-containing cupin 1vj2 (Zscr=13), the putative decarboxylase 1o4t (Zscr=12), 2pfw and the auxin binding protein 1lr5 (Zscr=11). Based on both SSM alignment and FFAS alignment, 3es1 is structurally similar to 1LR5 and 1FI2 . There is one 3es1 molecule in each asymmetric unit. The interface interaction suggests that the likely biomolecule of 3es1 is a dimer.

      

      

    391033_1.png

    Figure 1. 3es1 structure belongs to the CUPIN-2 superfamily and consists of β-strands mainly. 

      

    391033_2.png

    Figure 2. The biomolecule of 3es1 is a dimer based on interface interaction.

      

    391033_3.png

    Figure 3. 3es1 structure (green) is structurally similar to 1FI2 and 1LR5.

     

    References

     1.    Woo, E.J.,  Dunwell, J.M.,  Goodenough, P.W.,  Marvier, A.C.,  Pickersgill, R.W.   (2000) Germin is a manganese containing homohexamer with oxalate oxidase and superoxide dismutase activities.  Nat.Struct.Biol.   7: 1036-1040   (PDB IFI2)

    2.    Woo, E.J.,  Marshall, J.,  Bauly, J.,  Chen, J.G.,  Venis, M.,  Napier, R.M.,  Pickersgill, R.W.  (2002) Crystal structure of auxin-binding protein 1 in complex with auxin.  EMBO J.  21: 2877-2885  (PDB 1LR5)
     

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

      

    Ligand Summary

    Reviews

    References

     

    No references found.

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