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Structure of IDP02398

Crystal Structure of Cytsol Aminopeptidase fromFrancisella tularensis

Edit deposit information
CSGID target
IDP02398 
PDB Id
3PEI (NCBI MMDB
Authors
N.Maltseva,Y.Kim,M.Gu,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Oct 26, 2010 
Release Date
Dec 01, 2010 

Annotation

Description
Cytosol aminopeptidases belong to the peptidase M17 family and are involved in the processing and regular turnover of intracellular proteins. Aminopeptidases catalyze the removal of the unsubstituted N-terminal amino acid from various proteins and small peptides. They are widely distributed among prokaryotes and eukaryotes and typically are hexameric enzymes. In known cases each of six subunits contains two Zn2+/Mn 2+ ions in the active site, which are fundamental for catalytic activity and exhibit different metal ion exchange kinetics. In the apo form structure subunits that form the hexamer contain two domains with mixed α/β structure that are linked by a long α-helix. The loop (residues 258-269) which forms the part of the active site is disordered and there are no Zn2+/Mn 2+ ions found in the present structure. 
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 63 2 2  
Unit Cell

a=161.48Å, b=161.48Å, c=105.27Å
α=90.00, β=90.00, γ=120.00 
Solvent content
66.5  
Matthews coefficient
3.67  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
50.00-2.70Å (2.77-2.70Å)  
Rall(%)
16.7 
Rwork(%)
16.5 (22.1) 
Rfree(%)
21.0 (33.6) 
Num. observed reflections
22659 (1608) 
Num. Rfree reflections
1155 (94) 
Completeness(%)
99.7 (98.2) 

Model parameters

Num Atoms
4014  
Num Waters
366  
Num Hetatoms
0  
Model mean isotropic B factor
52.560Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.339°  
Filename uploaded
dep.pdb (uploaded on Oct 26, 2010 1:24 PM)  
Inserted
Oct 26, 2010