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 transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution. To be published
    Site JCSG
    PDB Id 1zyb Target Id 358851
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1406,NP_813211.1,, BV2565C, 282923 Molecular Weight 25433.14 Da.
    Residues 220 Isoelectric Point 6.17
    Sequence metmfdtllqlplfqglchedftsildkvklhfikhkagetiiksgnpctqlcfllkgeisivtnaken iytvieqieapyliepqslfgmntnyassyvahtevhtvciskafvlsdlfrydifrlnymnivsnraq nlysrlwdeptldlkskiirfflshcekpqgektfkvkmddlarclddtrlnisktlnelqdnglielh rkeilipdaqkll
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.15 Rfree 0.228
    Matthews' coefficent 3.86 Rfactor 0.177
    Waters 187 Solvent Content 67.86

    Ligand Information


    Google Scholar output for 1zyb
    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. De novo backbone scaffolds for protein design
    JT MacDonald, K Maksimiak - Proteins: Structure, , 2010 - Wiley Online Library
    3. Protein structural classification and family identification by multifractal analysis and wavelet spectrum
    SM Zhu, ZG Yu, A Vo - Chinese Physics B, 2011 - iopscience.iop.org

    Protein Summary

    This Bacteroides thetaiotaomicron descr protein belongs to the CRP (cAMP Receptor Protein) family of transcription regulators and contains a winged-helix-turn-helix DNA binding domain and a double stranded beta helix fold typical of a cAMP binding domain.

    Like CRP, 1zyb is made of an N- and C-terminal subdomains packed against the long dimerization alpha-helix (helix C) that connects them. While the architecture is similar, the precise arrangement of the three structural elements is considerably different when compared to both liganded and unliganded forms of CRP proteins, mostly due to a rotation of the C-terminal domain that results in the creation of an extended interdomain antiparallel beta-sheet and a concomitant shift of the alpha-helix away from the CRP N-terminal nucleotide binding site. Neither cAMP binding site appears to be conserved.

    The pdb entries structurally closest to 1zyb are PDB:2GAU and PDB:3E97 (DALI Z scores of 12.9 and 13.1 respectively), both rather more similar to other CRPs than to 1zyb.

    Ligand Summary





    No references found.

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