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 possible sugar phosphatase, HAD superfamily (ZP_00311070.1) from CYTOPHAGA HUTCHINSONII ATCC 33406 at 2.10 A resolution. To be published
    Site JCSG
    PDB Id 2hx1 Target Id 366867
    Molecular Characteristics
    Source Cytophaga hutchinsonii atcc 33406
    Alias Ids TPS1483,YP_679100.1, 104766 Molecular Weight 31272.26 Da.
    Residues 283 Isoelectric Point 5.17
    Sequence mqiesfksllpkykciffdafgvlktyngllpgientfdylkaqgqdyyivtndasrspeqladsyhkl glfsitadkiissgmitkeyidlkvdggivaylgtansanylvsdgikmlpvsaiddsnigevnalvll ddegfnwfhdlnktvnllrkrtipaivantdntypltktdvaiaiggvatmiesilgrrfirfgkpdsq mfmfaydmlrqkmeiskreilmvgdtlhtdilggnkfgldtalvltgntriddaetkikstgivpthic esaviel
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.10 Rfree 0.234
    Matthews' coefficent 2.37 Rfactor 0.179
    Waters 1035 Solvent Content 47.65

    Ligand Information


    Google Scholar output for 2hx1
    1. Assessment of predictions submitted for the CASP7 function prediction category
    G Lopez, A Rojas, M Tress - : Structure, Function, and , 2007 - Wiley Online Library
    2. 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
    3. Fams_ace: A combined method to select the best model after remodeling all server models
    G Terashi, M Takeda_Shitaka, K Kanou - Proteins: Structure, , 2007 - Wiley Online Library
    4. Domain definition and target classification for CASP7
    ND Clarke, I Ezkurdia, J Kopp, RJ Read - Proteins: Structure, , 2007 - Wiley Online Library
    5. Protein crystallography: a concise guide
    E Lattman, PJ Loll, P Loll - 2008 - books.google.com
    6. 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
    7. Reconstruction of Protein Backbone with the a-Carbon Coordinates
    JH Wang, CB Yang, CT Tseng - 2007 - asiair.asia.edu.tw
    8. Refinement of All-atom Backbone Prediction of Proteins
    HY Chang - 2008 - etd.lib.nsysu.edu.tw

    Protein Summary

    The YP_679100 (former ID: ZP_00311070) gene of C. hutchinsonii ATCC 33406 encodes a protein with sequence similarity to NagD proteins from COG0647 (predicted sugar phosphatases of the HAD superfamily). Similar proteins belong to all divisions of Life but viruses.

    In a cleft created by several highly conserved residues, there are two ligand molecules (from the crystallization medium: EPE and EDO) and a magnesium ion. Ligand EPE interacts with highly conserved Thr168 and Asp169. Among magnesium ion coordinated residues is highly conserved Asp232.

    The protein structure of YP_679100 is similar to members (i.e. found with FATCAT server PDB structure 1vjr) of SCOP family: NagD-like [102317]. The most structurally similar proteins are: putative NagD protein (PDB structure 1pw5; DALI Z-score 21.9; RMSD 3.3; 25% sequence identity within 239 superimposed residues) and hydrolase (PDB structure 2ho4; DALI Z-score 19.8; RMSD 4.1; 24% sequence identity within 231 superimposed residues).

    Analysis of the crystallographic packing of FG7288A using the PQS server {Henrick, 1998 #73} indicates that a tetramer is the biologically relevant form.

    Ligand Summary

    Similar proteins are annotated as 'pyridoxal phosphate phosphatase (PLP phosphatase)' but PLP was not co-crystallized with this protein.





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