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Structure of IDP00047

1.6 Angstrom resolution crystal structure of putative streptothricin acetyltransferase from Bacillus anthracis str. Ames in complex with acetyl coenzyme A

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CSGID target
IDP00047 
PDB Id
3PP9 (NCBI MMDB) 
Authors
A.S.Halavaty,Z.Wawrzak,O.Onopriyenko,A.Edwards,A.Savchenko,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Nov 24, 2010 
Release Date
Jan 12, 2011 

Annotation

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Description
The structure of the putative Se-Met streptothricin acetyltransferase from Bacillus anthracis str. Ames in complex with acetyl coenzyme A was solved by SAD. The protein is mostly β-stranded (40 %) with 20 % of the helical component. The core of the enzyme is a six-stranded antiparallel β-sheet, which ideal alignment is disrupted by the aliphatic tail of Acetyl-CoA. The tail mimics β-strand-β-strand hydrogen bonding interactions, making the sheet quasi seven-stranded. Each of three copies of the protein binds a single Acetyl-CoA molecule, which electron density is well defined. The chains B and C form a dimer with the buried surface area of 2140 A2, whereas chain A makes identical dimer with a symmetry related molecule with 2480 A2 of buried surface area. Monomers in the dimer interact such a way that a six-stranded antiparallel β-sheet is formed.  
Functional assignment
Transferase 
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
    K Potassium crystallization
    PO4 phosphate ion crystallization
    ACO acetyl coenzyme A biological
    MSE selenomethionine modified residue

    Structure information

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    Unit cell parameters

    Space Group
    C 1 2 1  
    Unit Cell

    a=47.10Å, b=68.01Å, c=174.17Å
    α=90.00, β=97.61, γ=90.00  
    Solvent content
    41.18  
    Matthews coefficient
    2.09  

    Refinement

    Data for the highest resolution shell is in parentheses.
    Resolution range
    29.28-1.60Å (1.64-1.60Å)  
    Rall(%)
    19.0  
    Rwork(%)
    18.9 (22.9)  
    Rfree(%)
    22.2 (25.1)  
    Num. observed reflections
    70882 (4357)  
    Num. Rfree reflections
    3544 (218)  
    Completeness(%)
    98.4 (82.9)  

    Model parameters

    Num Atoms
    4568  
    Num Waters
    355  
    Num Hetatoms
    686  
    Model mean isotropic B factor (Å2)
    28.640  
    RMSD bond length (Å)
    0.010  
    RMSD bond angle
    1.591°  
    Filename uploaded
    3PP9.pdb (uploaded on Sep 28, 2011 11:11 AM)  
    Inserted
    Dec 06, 2010