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The Open Protein Structure Annotation Network
PDB Keyword
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2rd9

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title Crystal structure of YfiT-like putative metal-dependent hydrolase (NP_241052.1) from Bacillus halodurans at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 2rd9 Target Id 376341
    Molecular Characteristics
    Source Bacillus halodurans c-125
    Alias Ids TPS1674,NP_241052.1, 383101 Molecular Weight 20362.13 Da.
    Residues 174 Isoelectric Point 5.66
    Sequence mnfqmneaiqllertpktlevfleglsdswhqcnegyetwtvyevvvhlieaektnwiprlrfilqege hkpfpafdrfshlnqsnavpiserfkefqqlrkenlntlrslvqseadlertgahpafgvvkvrellsa wvvhdlthiaqivrsmakrydtdvgpwkeylgilnd
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.30 Rfree 0.201
    Matthews' coefficent 2.91 Rfactor 0.152
    Waters 556 Solvent Content 57.74

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2rd9
    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. The structure of DinB from Geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily
    DR Cooper, K Grelewska, CY Kim - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    The BH0186 gene (PF05163, cl10108) from Bacillus halodurans encodes the NP_241052 protein, a YfiT-like putative metal-dependent hydrolase. HHPred and FFas show significant hits to DinB-like protein sequences. BH0186 genomic neighborhood contains the presence of a sorbitol dehydrogenase (BH1087).

    Pre-SCOP classifies 2rd9 in the all alpha class, DinB/YfiT-like putative metalloenzymes superfamily, YfiT-like putative metal-dependent hydrolase family. DALI top hit is with the YfiT protein 1rxq (Z=16), the TTHA0303 protein 2yqy (Z=12), and the DinB-like protein 3di5 (Z=11). A Ni ion per chain is found in the 2rd9 crystal structure. The metal binding residues are His48, His146, and His142. The N-terminal His-tag is part of the metal binding site in this structure, contributing a His side chain.

    Ligand Summary



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