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Structure of IDP90626

1.02 Angstrom resolution crystal structure of 3-phosphoshikimate 1- carboxyvinyltransferase from Vibrio cholerae in complex with shikimate-3-phosphate (partially photolyzed) and glyphosate.

Edit deposit information
CSGID target
IDP90626 
PDB Id
3NVS (NCBI MMDB
Authors
G.Minasov,S.H.Light,A.Halavaty,G.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Jul 08, 2010 
Release Date
Jul 21, 2010 

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. 3-phosphoshikimate 1- carboxyvinyltransferase is the sixth enzyme in the shikimate pathway and catalyzes the conversion of shikimate-3-phosphate and phosphoenolpyruvate to 5-enolpyruvyl-3-shikimate phosphate. This protein was co-crystallized with the substrate shikimate-3-phosphate and the commercially successful herbicide glyphosate. The enzyme consists of six βαβαββ motifs, three in both N- and C-terminal domains. The ultrahigh resolution of this structure provides an exquisite view of the mode of shikimate-3-phosphate and glyphosate binding. Glyphosate is observed to bind adjacent to shikimate-3-phosphate in phosphoenolpyruvate’s binding site.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
S3P shikimate-3-phosphate biological
GPJ glyphosate biological
MG
CL CHLORIDE ION
EPE
PO4 PHOSPHATE ION
SKM

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=43.87Å, b=87.48Å, c=49.99Å
α=90.00, β=105.26, γ=90.00 
Solvent content
35.02  
Matthews coefficient
1.89  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
14.89-1.02Å (1.05-1.02Å)  
Rall(%)
11.5 
Rwork(%)
11.4 (21.3) 
Rfree(%)
13.8 (23.5) 
Num. observed reflections
178385 (12825) 
Num. Rfree reflections
8919 (620) 
Completeness(%)
97.2 (95.3) 

Model parameters

Num Atoms
3632  
Num Waters
747  
Num Hetatoms
905  
Model mean isotropic B factor
8.510Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.542°  
Filename uploaded
rcsb060340.pdb (uploaded on Jul 13, 2010 5:55 PM)  
Inserted
Jul 13, 2010