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Structure of IDP01195

2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP

Edit deposit information
CSGID target
IDP01195 
PDB Id
3SC6 (NCBI MMDB
Authors
A.S.Halavaty,M.Kuhn,L.Shuvalova,G.Minasov,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jun 07, 2011 
Release Date
Jun 22, 2011 

Annotation

Description
dTDP-L-rhamnose is the activated sugar that is used in the synthesis of capsular polysaccharides in gram positive bacteria and O-antigens of gram negative bacteria. This molecule is synthesized by a series of four enzymes in the dTDP-L-rhamnose biosynthetic pathway. The last enzyme of the pathway, dTDP-4-dehydrorhamnose reductase, catalyzes the production of NADP and dTDP-L-rhamnose from NADPH and dTDP-4-dehydro-6-deoxy L-mannose. There are 6 molecules in the P21 asymmetric unit of the 2.65 Å resolution crystal structure of the dTDP-4-dehydrorhamnose reductase from Bacillus anthracis. Six subunits form two head-to-head trimers. Larger Rossmann-fold catalytic domains are at the oligomerization interface in each timer, whereas smaller hood domains of one timer face these domains in another trimer. Pairwise structural alignment of the subunits reveals movement of the hood domains. When two trimers are superimposed, the biggest rmsd value is 0.9 between two individual chains from each of the trimers. All six subunits have NADP bound.  
Functional assignment
Oxidoreductase 

Ligands

Ligand code Name Ligand type
NAP 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=79.45Å, b=113.34Å, c=144.95Å
α=90.00, β=91.18, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.90-2.65Å (2.72-2.65Å)  
Rall(%)
21.7 
Rwork(%)
21.5 (33.8) 
Rfree(%)
25.8 (40.7) 
Num. observed reflections
74606 (5411) 
Num. Rfree reflections
3730 (277) 
Completeness(%)
99.9 (99.5) 

Model parameters

Num Atoms
13672  
Num Waters
240  
Num Hetatoms
662  
Model mean isotropic B factor
56.690Å2  
RMSD bond length
0.006Å  
RMSD bond angle
1.359°  
Filename uploaded
3SC6.pdb (uploaded on Sep 28, 2011 11:02 AM)  
Inserted
Jun 09, 2011