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Structure of IDP04466

Crystal Structure of L-asparaginase I from Yersinia pestis

Edit deposit information
CSGID target
IDP04466 
PDB Id
3NTX (NCBI MMDB
Authors
Y.Kim,M.Gu,J.Hasseman,W.F.Anderson,A.Joachimiak 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 05, 2010 
Release Date
Aug 04, 2010 

Annotation

Description
This enzyme catalyses the deamination of asparagine to yield aspartic acid and an ammonium ion, resulting in a depletion of free circulatory asparagine in plasma. The enzyme from Yersinia pestis is type I L-asparageinase. The overall fold is similar to that of type II L-asparageinase of homotetrameric (dimer of intimate dimers) and the most of catalytic residues are conserved. However type I enzyme is just an intimate dimer, a half of that of type II L-asparageinase. The other key difference is the presence of the active-site flexible loop spanning a 14 – 28 beta-hairpin in the N-terminus including catalytic residues Thr14 and Tyr24. In type II enzyme, this loop serves as a mobile gate to the active site suggesting that in type I, this loop also serves as a gate but more restrictively. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
GOL
MSE modified residue

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=125.38Å, b=109.09Å, c=58.22Å
α=90.00, β=117.63, γ=90.00 
Solvent content
47.45  
Matthews coefficient
2.34  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
38.92-1.90Å (1.97-1.90Å)  
Rall(%)
15.6 
Rwork(%)
15.4 (21.1) 
Rfree(%)
19.2 (23.8) 
Num. observed reflections
56883 (5146) 
Num. Rfree reflections
2889 (249) 
Completeness(%)
99.2 (95.0) 

Model parameters

Num Atoms
5968  
Num Waters
503  
Num Hetatoms
0  
Model mean isotropic B factor
37.900Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.245°  
RMSD dihedral angle
15.274°
 
Filename uploaded
dep1w.pdb (uploaded on Jul 05, 2010 9:06 PM)  
Inserted
Jul 05, 2010