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Structure of IDP00122

Crystal structure of putative glycerate kinase 2 from Salmonella typhimurium LT2

Edit deposit information
CSGID target
IDP00122 
PDB Id
3CWC (NCBI MMDB
Authors
J.Osipiuk,M.Zhou,D.Holzle,W.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Apr 21, 2008 
Release Date
Jul 08, 2008 

Annotation

Description
Phosphorylation of glycerate by glycerate kinase is a key biochemical step connected with central carbon metabolism. Glycerate kinases have been characterized from all domains of life: Bacteria, Eukarya and Archaea. Two distinct classes of glycerate kinases were identified based on the reaction product - either 3-phosphoglycerate (3-PG) or 2-phoshoglycerate (2-PG). Despite the classification, 2-PG and 3-PG are easily interconverted by a phosphoglycerate mutase (PGM). There are also two protein classes of putative glycerate kinases based on structure similarities. These two separate fold families have no significant sequence similarity despite their identical biochemical activities. One family contains enzymes from bacterial species. The second family consists of proteins from eukaryotes and archaea in addition to several different bacterial species. Our structure belongs to the first structural class and is represented by glxK from Escherichia coli and glycerate kinase from Neisseria meningitidis. The N-terminal domain of the structure contains a 6-stranded parallel β-sheet and several surrounding helices with Rossmann-like topology. The C-terminal domain contains a central 5-stranded mixed β-sheet and 2 pairs of surrounding helices. The active site is likely to be inside the cleft between the two domains.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
EDO
MSE modified residue
CL CHLORIDE ION

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=63.73Å, b=59.55Å, c=103.61Å
α=90.00, β=106.01, γ=90.00 
Solvent content
47.73  
Matthews coefficient
2.35  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
49.81-2.23Å (2.28-2.23Å)  
Rall(%)
19.1 
Rwork(%)
18.8 (27.5) 
Rfree(%)
23.7 (33.2) 
Num. observed reflections
38556 (2619) 
Num. Rfree reflections
1927 (139) 
Completeness(%)
99.6 (96.2) 

Model parameters

Num Atoms
5293  
Num Waters
153  
Num Hetatoms
274  
Model mean isotropic B factor
38.090Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.547°  
Filename uploaded
3cwc.pdb (uploaded on Oct 27, 2008 1:44 PM)  
Inserted
Oct 27, 2008