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 haloacid delahogenase-like family hydrolase (NP_639141.1) from Xanthomonas campestris at 1.81 A resolution. To be published
    Site JCSG
    PDB Id 2pke Target Id 371319
    Molecular Characteristics
    Source Xanthomonas campestris pv. campestris str. atcc 33913
    Alias Ids TPS1580,NP_639141.1, 93087 Molecular Weight 27718.75 Da.
    Residues 250 Isoelectric Point 4.69
    Sequence mtpiaqrdgqaiqlvgfdgddtlwksedyyrtaeadfeailsgyldlgdsrmqqhllaverrnlkifgy gakgmtlsmietaieltearieardiqriveigratlqhpveviagvreavaaiaadyavvlitkgdlf hqeqkieqsglsdlfprievvsekdpqtyarvlsefdlpaerfvmignslrsdvepvlaiggwgiytpy avtwaheqdhgvaadeprlrevpdpsgwpaavraldaqagrqq
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.81 Rfree 0.229
    Matthews' coefficent 1.99 Rfactor 0.178
    Waters 257 Solvent Content 38.28

    Ligand Information


    Google Scholar output for 2pke
    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

    Protein Summary

    The XCC3796 gene translates into the aa sequence (NP_639141) that belongs to the HaloAcid Dehalogenase-like (HAD) hydrolase group (PF00702). It shows a signature motif (D18-D20) near the N-terminus involved in metal chelation. In 2pke dimeric structure, a Mg ion per molecule is bound by residues D18, D20, N186 and three ordered water molecules. Genome context analysis by STRING reveals a weak hit (score 0.63) with a ferrochelatase (NP_639434).


    SCOP classifies 2pke in the alpha/beta class, HAD-like superfamily, beta-phosphoglucomutase-like family. Strong structural similarity (FFAS scr=-76; Dali Z-scr=28; FATCAT P-val=1e-11) is detected with 3ddh, a putative bacterial HAD hydrolase with Mg bound, and with 2gfh, a mouse HAD-like homolog. A third yet significant hit (FFAS scr=-68; FATCAT P-val=1e-9) is seen with 1x42, a member of the HAD-related family [Ref].

    Ligand Summary





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