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3pgv

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

    Title Crystal structure of a haloacid dehalogenase-like hydrolase (KPN_04322) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 2.39 A resolution. To be published
    Site JCSG
    PDB Id 3pgv Target Id 388334
    Molecular Characteristics
    Source Klebsiella pneumoniae subsp. pneumoniae mgh 78578
    Alias Ids TPS7512,YP_001337957.1, 60679758, 91403 Molecular Weight 30083.58 Da.
    Residues 266 Isoelectric Point 5.27
    Sequence myqvvasdldgtllspdhfltpyaketlklltarginfvfatgrhyidvgqirdnlgirsymitsngar vhdsdgqqifahnldrdiaadlfeivrndpkivtnvyredewymnrhrpeemrffkeavfnyklyepge ldpqgiskvfftcedhehllpleqamnarwgdrvnvsfstltclevmaggvskghaleavakmlgytls dciafgdgmndaemlsmagkgcimanahqrlkdlhpelevigsnaddavprylrklyld
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.39 Rfree 0.2106
    Matthews' coefficent 2.35 Rfactor 0.1666
    Waters 428 Solvent Content 47.68

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     Target ID 388344 belongs to the Hydrolase_3 (PF08282) Pfam family. The Pfam family include members of the haloacid-dehalogenase-like hydrolases (HAD), a diverse group of enzymes The Haloacid Dehydrogenase (HAD) superfamily includes phosphatases, phosphonatases, P-type ATPases, beta-phosphoglucomutases, phosphomannomutases, and dehalogenases, which are involved in a variety of cellular processes ranging from amino acid biosynthesis to detoxification (see [Ref], [Ref], [Ref] for reviews).

     

    monomer.png

    Shown to the right is a ribbons representation of the structure of target ID 388344 with the N-terminal region in blue and the C-terminal region in red. Shown as a grey sphere is a magnesium atom modeled into the structure. The modeling of magnesium is supported by the presence of a similarly-bound magnesium in related structures. A molecule of HEPES from the crystallization buffer was also modeled into the structure and is shown by a stick representation.

     

     

     

     

    A DALI search shows that the structure of target ID 388344 reported here is similar to the following structures:

    PDB ID
    DALI Z-Score
    rmsd overlap (Ang)
    number of aligned residues
    % sequence ID
    Description
    Citation
    Hit Contains Mg?
    1rkq_A 31.4 2.2 252/271 29 Crystal structure of HAD-like phosphatase yidA from E. coli New York Structural Genomics Research Consortium  
    1nrw_A 31.1 2.3 252/285 27 The structure of a HALOACID DEHALOGENASE-LIKE HYDROLASE FROM B. SUBTILIS Midwest Center for Structural Genomics  
    3dnp_A 30.1 2.5 250/275 22

    Crystal structure of Stress response protein yhaX from Bacillus subtilis

     
    Midwest Center for Structural Genomics  
    1rlo_D  29.7 2.1 246/268 20 Phospho-aspartyl Intermediate Analogue of ybiV from E. coli K12  [Ref]  
    1rlm_A 29.3 2.3 249/269 20 Crystal Structure of ybiV from Escherichia coli K12  [Ref]  
    1ymq_A 29.1 2.2 244/260 18 HAD Superfamily Phosphotransferase Substrate Diversification: Structure and Function Analysis of the HAD Subclass IIB Sugar Phosphatase BT4131   [Ref]  
    1rlt_C 28.9 2.3 246/268 28 Transition State Analogue of ybiV from E. coli K12  [Ref]  
    2rb5_A 28.9 2,3 245/261 18 X-ray Crystallographic Structures Show Conservation of a Trigonal-Bipyramidal Intermediate in a Phosphoryl-transfer Superfamily.  [Ref]  

     

     

     

     

     

     

     

    Ligand Summary

    Pfam:  This one belongs to Pfam family Hydrolase_3

    Reviews

    References

     

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