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Structure of IDP90646

Crystal Structure of Probable Cytoplasmic L-asparaginase fromCampylobacter jejuni

Edit deposit information
CSGID target
IDP90646 
PDB Id
3NXK (NCBI MMDB
Authors
Y.Kim,M.Makowska-Grzyska,N.Maltseva,L.Papazisi,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 14, 2010 
Release Date
Aug 04, 2010 

Annotation

Description
L-Asparaginase, which is found in various plant, animal and bacterial cells, catalyses the deamination of asparagine to yield aspartic acid and an ammonium ion, resulting in a depletion of free circulatory asparagine in plasma. The structure of the asparaginase from Campylobacter jejuni forms a tight homotetramer, dimer of intimate dimers with 222 symmetry similar to that of L-asparaginase from Erwinia chrysanthemi. Each of the four active sites of l-asparaginase is located between the N- and C-terminal domains of two adjacent monomers. The flexible part of the active site consists of several residues (positions 16−34), referred to as the active site flexible loop, and covers the binding pocket upon substrate binding to the enzyme. The nucleophile, Thr16, is also located in the flexible loop region. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
SO4
ACY
GOL
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=73.32Å, b=127.65Å, c=149.83Å
α=90.00, β=103.05, γ=90.00 
Solvent content
48.15  
Matthews coefficient
2.37  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
36.91-2.40Å (2.48-2.40Å)  
Rall(%)
16.9 
Rwork(%)
16.6 (23.3) 
Rfree(%)
22.8 (30.4) 
Num. observed reflections
109638 (10070) 
Num. Rfree reflections
5470 (457) 
Completeness(%)
99.5 (96.0) 

Model parameters

Num Atoms
20585  
Num Waters
1060  
Num Hetatoms
72  
Model mean isotropic B factor
35.530Å2  
RMSD bond length
0.008Å  
RMSD bond angle
1.117°  
RMSD dihedral angle
14.462°
 
Filename uploaded
dep1w.pdb (uploaded on Jul 14, 2010 6:27 AM)  
Inserted
Jul 14, 2010