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Structure of IDP01182

2.31 Angstrom resolution crystal structure of a holo-(acyl-carrier-protein) synthase from Bacillus anthracis str. Ames in complex with CoA (3',5'-ADP)

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CSGID target
IDP01182 
PDB Id
3HYK (NCBI MMDB) 
Authors
A.S.Halavaty,G.Minasov,T.Skarina,O.Onopriyenko,L.Papazisi,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jun 22, 2009 
Release Date
Jun 30, 2009 

Annotation

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Description
Analysis of the initial 2Fo-Fc and difference electron density maps at each coenzyme binding site of the protein revealed the presence of two 3´,5´-ADP molecules instead of the CoA that was added during crystallization. One 3´,5´-ADP resembles the conformation of the ADP portion of CoA in the binary CoA-AcpS or 3´,5´-ADP-AcpS structures from the PDB. The position of the second 3´,5´-ADP has never been described before. Its unusual coordination depends in part on lattice packing and the high concentration of magnesium, which suggests two interesting questions. Is the position of the second ADP dictated by the chemistry of the AcpS-catalyzed reaction? Though presence of the second ADP in the vicinity of the active site is a crystallographic artifact, can it assist in the design of inhibitor(s)? The biological relevance of the second ADP should be further investigated. One paper was published: Acta Crystallogr D Biol Crystallogr. 2012 Oct;68(Pt 10):1359-70. 
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
CL chloride crystallization
MG magnesium biological
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

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Unit cell parameters

Space Group
P 32 2 1  
Unit Cell

a=77.53Å, b=77.53Å, c=122.97Å
α=90.00, β=90.00, γ=120.00 
Solvent content
53.19  
Matthews coefficient
2.63  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
34.99-2.31Å (2.37-2.31Å)  
Rall(%)
19.3 
Rwork(%)
19.0 (18.6) 
Rfree(%)
24.7 (27.2) 
Num. observed reflections
19292 (1363) 
Num. Rfree reflections
983 (64) 
Completeness(%)
99.5 (97.1) 

Model parameters

Num Atoms
2723  
Num Waters
260  
Num Hetatoms
531  
Model mean isotropic B factor
16.960Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.744°  
Filename uploaded
3HYK.pdb (uploaded on Sep 17, 2010 6:38 PM)  
Inserted
Jun 22, 2009