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 BH3980 (10176605) from BACILLUS HALODURANS at 2.04 A resolution. To be published
    Site JCSG
    PDB Id 2hh6 Target Id 361188
    Molecular Characteristics
    Source Bacillus halodurans c-125
    Alias Ids TPS1465,10176605, PF06304, 90565 Molecular Weight 12901.04 Da.
    Residues 112 Isoelectric Point 6.13
    Sequence msfiekmigslndkrewkamearakalpkeyhhaykaiqkymwtsggptdwqdtkrifggildlfeega aegkkvtdltgedvaafcdelmkdtktwmdkyrtklndsigrd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 2.04 Rfree 0.238
    Matthews' coefficent 5.26 Rfactor 0.224
    Waters 78 Solvent Content 76.43

    Ligand Information


    Google Scholar output for 2hh6
    1. Macromolecular modeling with rosetta
    R Das, D Baker - Annu. Rev. Biochem., 2008 - annualreviews.org
    2. High-resolution structure prediction and the crystallographic phase problem
    B Qian, S Raman, R Das, P Bradley, AJ McCoy - Nature, 2007 - nature.com
    3. Practically useful: what the Rosetta protein modeling suite can do for you
    KW Kaufmann, GH Lemmon, SL DeLuca - Biochemistry, 2010 - ACS Publications
    4. Protein structure prediction and model quality assessment
    A Kryshtafovych, K Fidelis - Drug discovery today, 2009 - Elsevier
    5. 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
    6. On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination
    S Panjikar, V Parthasarathy, VS Lamzin - Section D: Biological , 2009 - scripts.iucr.org
    7. Domain definition and target classification for CASP7
    ND Clarke, I Ezkurdia, J Kopp, RJ Read - Proteins: Structure, , 2007 - Wiley Online Library
    8. Alternate states of proteins revealed by detailed energy landscape mapping
    MD Tyka, DA Keedy, I Andr, F DiMaio, Y Song - Journal of molecular , 2011 - Elsevier
    9. A coarse-grained Langevin molecular dynamics approach to de novo protein structure prediction
    TN Sasaki, H Cetin, M Sasai - Biochemical and biophysical research , 2008 - Elsevier
    10. Reconstruction of Protein Backbone with the alpha-Carbon Coordinates
    JH Wang, CB Yang, CT Tseng - Journal of Information Science , 2010 - etd.lib.nsysu.edu.tw
    11. Reconstruction of Protein Backbone with the a-Carbon Coordinates
    JH Wang, CB Yang, CT Tseng - 2007 - asiair.asia.edu.tw
    12. Refinement of All-atom Backbone Prediction of Proteins
    HY Chang - 2008 - etd.lib.nsysu.edu.tw

    Protein Summary

    The gene BH3980 from Bacillus halodurans probably encodes the NP_244848 protein, a transcriptional regulator from the DUF1048 group (PF06304), homologous to PadR 3HHH (sequence identity with YP_003354695 is 44%) and LmrR 3F8B families of transcription regulators.  

    SCOP classifies 2hh6 inside the left-handed superhelix fold, BH3980-like (super)family. DALI only provides weak hits (Z=10) with the BH3976 protein 2o4t and 2o3l. The structure comparison searches using 2hh6 as query demonstrates significant similarities to these transcription regulators, although several structural features differ. PadR acts as a repressor of padA gene expression in the phenolic acid stress response, which is important in plant-soil ecosystems.  LmrR is PadR-related transcriptional repressor that regulates the production of LmrCD, a major multidrug ABC transporter in Lactococcus lactis. Transcriptional regulation is presumed to follow a drug-sensitive induction mechanism involving the direct binding of transporter ligands to LmrR.

    Ligand Summary





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