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Structure of IDP01880

1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2

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CSGID target
IDP01880 
PDB Id
3OGA (NCBI MMDB) 
Authors
A.S.Halavaty,G.Minasov,L.Shuvalova,J.Winsor,I.Dubrovska,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Aug 16, 2010 
Release Date
Oct 06, 2010 

Annotation

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Description
The 1.75 A resolution structure of the wild type IDP01880 protein was solved by molecular replacement using the structure of this protein (PDB ID 3N77) with three point mutations (K118A, E120A, E121A) as a model. It is interesting to note that both structures have different crystal packing, which might be a result of site-directed mutagenesis. Pairwise structural alignment clearly shows that the residues Lys188, Glu120 and Glu121 if not mutated would clash with the Leu63-Ile66 stretch of residues of symmetry related molecule in the 3N77 structure. Residues 25 through 30 in chain A of the 3OGA structure are disordered, whereas they are built in chain B. These residues constitute a loop, which conformation is different from that of the mutant structure. Additionally, residues 78 through 88 in chain B and residues 82-83 in chain A of the wild type structure are disordered.  
Functional assignment
Hydrolase 
Slides:
  • Asymmetric unit
  • Biological unit
  • B-factors distribution
  • B-factors distribution on the surface
  • Homolog superposition
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    secondary structure, N to C, molecule

    Ligands

    Ligand code Name Ligand type
    BME beta-mercaptoethanol crystallization
    PO4 phosphate ion biological

    Structure information

    View structure information | Edit structure information (upload a PDB file)

    Unit cell parameters

    Space Group
    P 21 21 21  
    Unit Cell

    a=41.59Å, b=81.10Å, c=110.08Å
    α=90.00, β=90.00, γ=90.00  
    Solvent content
    49.48  
    Matthews coefficient
    2.43  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    29.03-1.75Å (1.80-1.75Å)  
    Rall(%)
    18.7  
    Rwork(%)
    18.5 (21.7)  
    Rfree(%)
    21.8 (24.9)  
    Num. observed reflections
    38165 (2700)  
    Num. Rfree reflections
    1908 (141)  
    Completeness(%)
    99.5 (96.9)  

    Model parameters

    Num Atoms
    2292  
    Num Waters
    237  
    Num Hetatoms
    291  
    Model mean isotropic B factor (Å2)
    37.450  
    RMSD bond length (Å)
    0.012  
    RMSD bond angle
    1.502°  
    Filename uploaded
    3OGA.pdb (uploaded on Sep 28, 2011 11:24 AM)  
    Inserted
    Aug 18, 2010