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The Open Protein Structure Annotation Network
PDB Keyword
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4kw2

    Title Crystal structure of a Putative uncharacterized protein (BDI_1873) from Parabacteroides distasonis ATCC 8503 at 2.32 A resolution. To be published
    Site JCSG
    PDB Id 4kw2 Target Id 396613
    Molecular Characteristics
    Source Parabacteroides distasonis atcc 8503
    Alias Ids TPS29570,YP_001303230.1, 534432 Molecular Weight 28041.63 Da.
    Residues 246 Isoelectric Point 5.87
    Sequence adwkvgiqtwtfhnltlmetldktqqlgmgyaeafffqelgapfpketylnydlsddncallrhefkir gikpiafgvasygtneewdkffafahkigahivtvepelnqldyieslakkydmevaihnhpspciyas aevvekalkgrsplmgvcadighwkrvgedplknlqklsgrikvahlkdltdkmedatwgtgilpvkaf vnelkrqhfnglisieyddfksdiqeirnsleflqkcsk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.32 Rfree 0.2196
    Matthews' coefficent 2.72 Rfactor 0.1829
    Waters 83 Solvent Content 54.79

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    The protein YP_001303230.1 does not have a functional characterization.

    YP_001303230.1 belongs to PFAM PF01261 AP_endonuc_2. According to PFAM "This TIM alpha/beta barrel structure is found in xylose isomerase (P19148) and in endonuclease IV (P12638 EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae."

    The monomer structure is shown below in rainbow representation.

    PX15447A.png

    The biological assembly could be a trimer according to crystal packing analysis.

    PX15447A_trimer.png

    Top 10 DALI Structural Homologs
     
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 3p6l 26.4 2.3 225 262 33 Sugar Phosphate Isomerase/epimerase
    2 3lmz 22.5 2.7 216 251 26 Putative Sugar Isomerase
    3 3cqj 18.8 3.2 213 275 18 L-ribulose-5-phosphate 3-epimerase Ulae
    4 3vnl 18.7 2.6 211 291 14 Xylose Isomerase Domain Protein Tim Barrel
    5 3cqk 18.7 3.2 213 276 18 L-ribulose-5-phosphate 3-epimerase Ulae
    6 3vnj 18.6 2.6 211 290 14 Xylose Isomerase Domain Protein Tim Barrel
    7 3vni 18.6 2.6 211 289 14 Xylose Isomerase Domain Protein Tim Barrel
    8 3cqi 18.6 3.2 212 273 18 L-ribulose-5-phosphate 3-epimerase Ulae
    9 2qun 18.6 2.6 211 290 18 D-tagatose 3-epimerase
    10 2qum 18.6 2.6 211 290 18 D-tagatose 3-epimerase

     

    Superposition with top two DALI hits

    PX15447A_3p6l.png PX15447A_3lmz.png
    YP_001303230.1 (green) on 3p6l (blue) YP_001303230.1 (green) on 3lmz (blue)

    Ligand Summary

    Reviews

    References

     

    No references found.

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