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Structure of IDP90792

2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH

Edit deposit information
CSGID target
IDP90792 
PDB Id
3SEF (NCBI MMDB
Authors
A.S.Halavaty,S.H.Light,G.Minasov,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jun 10, 2011 
Release Date
Jul 27, 2011 

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 dehydrogenase is an NADPH-dependent monomeric enzyme which catalyzes the conversion of dehydroshikimate to shikimate, the fourth step in the shikimate pathway. This structure reveals the reaction product shikimate bound to the N-terminal domain and has an alternating β-strand/α-helix character. Whereas, the C-terminal NADPH binding domain adopts a classical Rossman fold.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
NDP Nicotinamide adenine dinucleotide phosphate biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=76.03Å, b=86.08Å, c=81.02Å
α=90.00, β=92.85, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.48-2.40Å (2.46-2.40Å)  
Rall(%)
23.7 
Rwork(%)
23.5 (29.5) 
Rfree(%)
27.6 (38.0) 
Num. observed reflections
41015 (2981) 
Num. Rfree reflections
2050 (141) 
Completeness(%)
99.7 (97.7) 

Model parameters

Num Atoms
8129  
Num Waters
134  
Num Hetatoms
255  
Model mean isotropic B factor
57.940Å2  
RMSD bond length
0.005Å  
RMSD bond angle
1.267°  
Filename uploaded
3SEF.pdb (uploaded on Jun 04, 2015 4:24 PM)  
Inserted
Jun 10, 2011