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Structure of IDP90820

D-Erythronate-4-Phosphate Dehydrogenase complexed with NAD from Salmonella typhimurium LT2

Edit deposit information
CSGID target
IDP90820 
PDB Id
3OET (NCBI MMDB
Authors
E.V.Filippova,Z.Wawrzak,O.Onopriyenko,A.Savchenko,A.Edwards,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Ekaterina Filippova 
Responsible lab
Northwestern University 
Deposition Date
Aug 13, 2010 
Release Date
Aug 25, 2010 

Annotation

Description
The enzyme erythronate-4-phosphate dehydrogenase, encoded by the pdxB gene, catalyses the conversion of erythronate-4-phosphate to 3-hydroxy-4-phospho-hydroxy-α-ketobutyrate. It belongs to the d-isomer-specific 2-hydroxyacid dehydrogenase family. It is essential for de novo biosynthesis of vitamin B6 (pyridoxine). Crystal structure of erythronate-4-­phosphate dehydrogenase from Salmonella typhimurium LT2 has eight protein molecules in the asymmetric part of the unit cell. Each protein molecule consists of three structural domains: the lid domain, the nucleotide-binding domain, and the C-terminal domain. The latter domain has a unique fold and is largely responsible for dimerization. Interestingly, in all protein molecules of the enzyme the C-terminal domain displays significantly different conformations. The NAD was found in the active site bound to the nucleotide-binding domain. Our structural data allow a detailed understanding of cofactor recognition site, and provide insights into PdxB catalysis. 
Functional assignment
Oxidoreductase 

Ligands

Ligand code Name Ligand type
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=93.28Å, b=167.76Å, c=103.95Å
α=90.00, β=93.88, γ=90.00 
Solvent content
49.25  
Matthews coefficient
2.42  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.19-2.36Å (2.42-2.36Å)  
Rall(%)
19.3 
Rwork(%)
19.0 (22.6) 
Rfree(%)
25.3 (31.3) 
Num. observed reflections
128763 (8615) 
Num. Rfree reflections
6438 (438) 
Completeness(%)
98.6 (89.6) 

Model parameters

Num Atoms
22605  
Num Waters
556  
Num Hetatoms
1230  
Model mean isotropic B factor
46.670Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.460°  
Filename uploaded
rcsb061025.pdb (uploaded on Aug 17, 2010 1:21 PM)  
Inserted
Aug 17, 2010