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Structure of IDP01110

1.63 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose 3,5-epimerase (rfbC) from Bacillus anthracis str. Ames with TDP and PPi bound

Edit deposit information
CSGID target
IDP01110 
PDB Id
3RYK (NCBI MMDB
Authors
A.S.Halavaty,M.Kuhn,G.Minasov,L.Shuvalova,K.Kwon,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
May 11, 2011 
Release Date
May 25, 2011 

Annotation

Description
dTDP-4-dehydrorhamnose 3,5-epimerase is the third enzyme in the dTDP-L-rhamnose biosynthetic pathway, and catalyzes the conversion of dTDP-4-dehydro-6-deoxy-D-glucose to dTDP-4-dehydro-6-deoxy-L-mannose. This is an essential pathway in bacteria and is not present in humans. Therefore, it is considered a good target pathway for antimicrobial drug development. This protein is believed to form a complex with dTDP-4-dehydrorhamnose reductase, the fourth and final enzyme of the dTDP-L-rhamnose pathway. The crystal structure of the Bacillus anthracis epimerase was determined by molecular replacement and refined to 1.63 Å resolution. The protein is predominantly beta-stranded and has two domains: a short N-terminal oligomerization domain and larger C-terminal catalytic domain. Two molecules in the asymmetric unit form a dimer through extensive antiparallel hydrogen-bonding interactions of a beta strand from the oligomerization domain and a beta strand of the catalytic domain. One epimerase molecule has TDP and another PPi bound in the active site.  
Functional assignment
Isomerase 

Ligands

Ligand code Name Ligand type
POP pyrophosphate 2- biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 3  
Unit Cell

a=86.65Å, b=86.65Å, c=45.10Å
α=90.00, β=90.00, γ=120.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.85-1.63Å (1.67-1.63Å)  
Rall(%)
12.5 
Rwork(%)
12.3 (15.3) 
Rfree(%)
16.0 (25.3) 
Num. observed reflections
47036 (3350) 
Num. Rfree reflections
2445 (201) 
Completeness(%)
99.8 (96.7) 

Model parameters

Num Atoms
2885  
Num Waters
266  
Num Hetatoms
309  
Model mean isotropic B factor
21.230Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.852°  
Filename uploaded
3RYK.pdb (uploaded on Sep 28, 2011 11:04 AM)  
Inserted
Jun 14, 2011