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Structure of IDP04176

2.5 Angstrom Resolution Crystal Structure of 3-Dehydroquinate Synthase (aroB) from Vibrio cholerae

Edit deposit information
CSGID target
IDP04176 
PDB Id
3OKF (NCBI MMDB
Authors
G.Minasov,S.H.Light,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
Aug 24, 2010 
Release Date
Sep 08, 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. Dehydroquinate synthase is a metalloprotein which catalyzes the nicotinamide adenine dinucleotide (NAD)-dependent conversion of 3-deoxy-7-phosphoheptulonate synthase to dehydroquinate, the second step in the shikimate pathway. This structure consists of an N-terminal NAD binding domain and an alpha-helical C-terminal domain. Clear electron corresponding to a bound NAD molecule is observed at the active site.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
NAD biological
PO4 PHOSPHATE ION
CL
NA Sodium ion

Structure information

Unit cell parameters

Space Group
P 43 21 2  
Unit Cell

a=80.14Å, b=80.14Å, c=262.96Å
α=90.00, β=90.00, γ=90.00 
Solvent content
50.56  
Matthews coefficient
2.49  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.62-2.50Å (2.56-2.50Å)  
Rall(%)
18.4 
Rwork(%)
18.2 (27.1) 
Rfree(%)
22.3 (31.3) 
Num. observed reflections
30650 (2194) 
Num. Rfree reflections
1563 (118) 
Completeness(%)
99.9 (99.4) 

Model parameters

Num Atoms
5426  
Num Waters
167  
Num Hetatoms
284  
Model mean isotropic B factor
41.900Å2  
RMSD bond length
0.009Å  
RMSD bond angle
1.295°  
Filename uploaded
rcsb061227.pdb (uploaded on Sep 08, 2010 12:08 AM)  
Inserted
Sep 08, 2010