Structure of IDP91206

1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides thetaiotaomicron.

Edit deposit information
CSGID target
IDP91206 
PDB Id
3VAA (NCBI MMDB
Authors
G.Minasov,S.H.Light,A.Halavaty,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Dec 29, 2011 
Release Date
Jan 18, 2012 

Annotation

Description
The shikimate pathway links metabolism of carbohydrates to biosynthesis of aromatic compounds. In a sequence of seven steps, phosphoenolpyruvate and erythrose 4-phosphate are converted to chorismate, a precursor of the aromatic amino acids and many secondary aromatic metabolites. The shikimate pathway is essential for most bacteria and plants but absent in humans, making it an attractive target for the development of novel antibiotics. Shikimate kinase catalyzes the fourth step in the pathway. The structure reveals distinct sites for ATP and shikimate. Interestingly, within the asymmetric unit's three molecules two conformational states of the ATP binding site and three states of the shikimate binding site are observed.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
BME crystallization
GOL crystallization
PEG crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=61.25Å, b=46.46Å, c=105.12Å
α=90.00, β=97.42, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.06-1.70Å (1.74-1.70Å)  
Rall(%)
16.5 
Rwork(%)
16.3 (25.3) 
Rfree(%)
19.9 (26.3) 
Num. observed reflections
64553 (4429) 
Num. Rfree reflections
3292 (204) 
Completeness(%)
99.4 (93.0) 

Model parameters

Num Atoms
4441  
Num Waters
453  
Num Hetatoms
504  
Model mean isotropic B factor
25.500Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.287°  
Filename uploaded
rcsb069792.pdb (uploaded on Jan 10, 2012 12:31 PM)  
Inserted
Jan 10, 2012