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Structure of IDP00951

2.14 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium in Complex with NADP.

Edit deposit information
CSGID target
IDP00951 
PDB Id
3KBO (NCBI MMDB
Authors
G.Minasov,Z.Wawrzak,T.Skarina,O.Onopriyenko,L.Papazisi,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Oct 20, 2009 
Release Date
Oct 27, 2009 

Annotation

Description
D-3-Phosphoglycerate dehydrogenase catalyzes the transition of 3-phosphoglycerate into 3-phosphohydroxypyruvate, which is the first and rate-limiting step in the phosphorylated pathway of serine biosynthesis, using NAD+/NADH as a cofactor. L-Serine is synthesized from glycolytic intermediate 3-phosphoglycerate and is an indispensable precursor for the synthesis of proteins, membrane lipids, nucleotides, and neuroactive amino acids D-serine and glycine.  
Functional assignment
Phosphoglycerate dehydrogenase, serine biosynthesis 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological
NDB Dimethyl(2 hydroxyethyl)ammonium propane sulfonate crystallization
EPE crystallization
CL CHLORIDE ION crystallization
MSE modified residue

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=279.62Å, b=45.59Å, c=112.33Å
α=90.00, β=101.58, γ=90.00 
Solvent content
49.88  
Matthews coefficient
2.45  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.93-2.14Å (2.20-2.14Å)  
Rall(%)
21.4 
Rwork(%)
21.1 (29.7) 
Rfree(%)
26.9 (32.3) 
Num. observed reflections
75670 (5217) 
Num. Rfree reflections
3783 (232) 
Completeness(%)
98.0 (92.5) 

Model parameters

Num Atoms
9974  
Num Waters
555  
Num Hetatoms
811  
Model mean isotropic B factor
27.210Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.453°  
Filename uploaded
valid-7-coot-1.pdb (uploaded on Oct 21, 2009 12:59 AM)  
Inserted
Oct 21, 2009