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Structure of IDP00951

2.1 Angstrom Crystal Structure of Putative Oxidoreductase (ycdW) from Salmonella typhimurium.

Edit deposit information
CSGID target
IDP00951 
PDB Id
3PP8 (NCBI MMDB
Authors
G.Minasov,Z.Wawrzak,T.Skarina,Y.Wang,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
Nov 24, 2010 
Release Date
Dec 08, 2010 

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

Structure information

Unit cell parameters

Space Group
C 2 2 21  
Unit Cell

a=40.49Å, b=139.37Å, c=111.04Å
α=90.00, β=90.00, γ=90.00 
Solvent content
43.91  
Matthews coefficient
2.19  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.51-2.10Å (2.15-2.10Å)  
Rall(%)
19.9 
Rwork(%)
19.7 (27.2) 
Rfree(%)
23.5 (31.4) 
Num. observed reflections
18802 (1361) 
Num. Rfree reflections
958 (70) 
Completeness(%)
99.8 (99.6) 

Model parameters

Num Atoms
2403  
Num Waters
82  
Num Hetatoms
146  
Model mean isotropic B factor
44.490Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.396°  
Filename uploaded
rcsb062650.pdb (uploaded on Dec 06, 2010 1:29 PM)  
Inserted
Dec 06, 2010