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Structure of IDP90717

Crystal structure of Phosphoglycerate Kinase from Campylobacter jejuni.

Edit deposit information
CSGID target
IDP90717 
PDB Id
3Q3V (NCBI MMDB
Authors
E.V.Filippova,Z.Wawrzak,O.Onopriyenko,A.Edwards,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Ekaterina Filippova 
Responsible lab
Northwestern University 
Deposition Date
Dec 22, 2010 
Release Date
Jan 12, 2011 

Annotation

Description
Phosphoglycerate kinase (PGK) is a key glycolytic enzyme that catalyzes the reversible transfer of a phosphate from 1,3-bisphosphoglycerate to ADP to form 3-phosphoglycerate and ATP in the presence of magnesium. PGK is essential in most living cells both for ATP generation in the glycolytic pathway of aerobes and for fermentation in anaerobes. The structure of PGK from Campylobacter jejuni has been determined to 2.15 A resolution. Like other kinases, PGK folds into two distinct domains, which undergo a large hinge-bending motion upon catalysis. The substrate binding sites, as deduced from electron density maps, are compatible with known substrate specificity and the stereochemical requirements for the enzymic reaction. The sulfate ion is found in the active site of the protein.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
SO4 biological
FMT crystallization
MSE modified residue
K crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 2  
Unit Cell

a=110.28Å, b=165.22Å, c=54.60Å
α=90.00, β=90.00, γ=90.00 
Solvent content
56.09  
Matthews coefficient
2.8  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.61-2.15Å (2.20-2.15Å)  
Rall(%)
19.0 
Rwork(%)
18.7 (24.9) 
Rfree(%)
23.7 (28.6) 
Num. observed reflections
54727 (3826) 
Num. Rfree reflections
2791 (200) 
Completeness(%)
98.4 (93.7) 

Model parameters

Num Atoms
5903  
Num Waters
323  
Num Hetatoms
514  
Model mean isotropic B factor
24.040Å2  
RMSD bond length
0.015Å  
RMSD bond angle
1.423°  
Filename uploaded
3Q3V.pdb (uploaded on Jan 12, 2011 12:28 PM)  
Inserted
Dec 22, 2010