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Structure of IDP90895

Crystal Structure of Nicotinate Phosphoribosyltransferasefrom Yersinia pestis

Edit deposit information
CSGID target
IDP90895 
PDB Id
3OS4 (NCBI MMDB
Authors
N.Maltseva,Y.Kim,M.Gu,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Sep 08, 2010 
Release Date
Sep 22, 2010 

Annotation

Description
Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and can act as an important substrate in numerous biological processes. Bacteria maintain its total NADH/NAD+ intracellular pool by synthesizing NAD through the de novo pathway and the pyridine nucleotide salvage pathway. The salvage pathway recycles intracellular NAD breakdown products and preformed pyridine compounds from the environment, such as nicotinic acid. The enzyme nicotinic acid phosphoribosyltransferase, encoded by the pncB gene, catalyzes the first reaction in the NAD salvage I pathway which involves nicotinamide deaminase (pncA), and nicotinate phosphoribosyltransferase (pncB ). Nicotinate phosphoribosyltransferase catalyzes the formation of nicotinate mononucleotide, a direct precursor of NAD, from nicotinic acid. This reaction is believed to be the rate-limiting step in the NAD salvage pathway. The Crystal Structure of Nicotinate Phosphoribosyltransferase from Yersinia pestis was solved at 1.9A. The structure reveals a possible three-domain alpha-beta fold and represents dimer. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
ACY crystallization
MG
GOL
PEG
FMT
CL
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 1  
Unit Cell

a=47.39Å, b=50.68Å, c=87.18Å
α=81.95, β=83.39, γ=71.95 
Solvent content
40.93  
Matthews coefficient
2.08  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
33.93-1.60Å (1.66-1.60Å)  
Rall(%)
16.3 
Rwork(%)
16.2 (23.0) 
Rfree(%)
19.3 (29.0) 
Num. observed reflections
93910 (6036) 
Num. Rfree reflections
2047 (141) 
Completeness(%)
91.6 (60.0) 

Model parameters

Num Atoms
7787  
Num Waters
870  
Num Hetatoms
68  
Model mean isotropic B factor
22.820Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.315°  
RMSD dihedral angle
14.628°
 
Filename uploaded
dep.pdb (uploaded on Sep 08, 2010 12:35 PM)  
Inserted
Sep 08, 2010