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Structure of IDP01334

N-acetylglucosamine-6-phosphate deacetylase from Vibrio cholerae complexed with fructose 6-phosphate.

Edit deposit information
CSGID target
IDP01334 
PDB Id
3IV8 (NCBI MMDB
Authors
J.Osipiuk,N.Maltseva,J.Stam,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Aug 31, 2009 
Release Date
Sep 08, 2009 

Annotation

Description
N-acetylglucosamine-6-phosphate deacetylases (NAGPase) catalyze the hydrolysis of N-acetyl-D-glucosamine-6-phosphate to form D-glucosamine-6-phosphate and acetate. Amino sugars, like glucosamine or N-acetylglucosamine are used by bacteria for cell wall and lipid A synthesis. Bacteria use also N-acetylglucosamine as a carbon source producing similar growth rates as glucose. The structure of IDP01334 closely resembles the structures of protein homologs from E.coli and B.subtilis. The protein monomer forms two structural domains. The bigger domain comprises the central part of the protein and forms an  barrel enclosing the catalytic site of the enzyme. The small domain consists of the N and C termini and forms a -strand barrel. Our structure includes a nickel ion in the position of one of two iron ions found in N-acetylglucosamine-6-phosphate deacetylase from Bacillus subtilis, 2VHL. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
F6P fructose-6-phosphate
SO4
NI

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=83.18Å, b=123.05Å, c=156.29Å
α=90.00, β=90.00, γ=90.00 
Solvent content
49.22  
Matthews coefficient
2.42  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
35.18-2.53Å (2.59-2.53Å)  
Rall(%)
18.6 
Rwork(%)
18.3 (26.6) 
Rfree(%)
25.3 (38.0) 
Num. observed reflections
54165 (3813) 
Num. Rfree reflections
2762 (187) 
Completeness(%)
99.6 (96.3) 

Model parameters

Num Atoms
11727  
Num Waters
332  
Num Hetatoms
0  
Model mean isotropic B factor
34.530Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.609°  
Filename uploaded
idp01334_f6p.pdb (uploaded on Sep 01, 2009 4:38 PM)  
Inserted
Sep 01, 2009