Structure of IDP91783

Crystal structure of aminoglycoside 4'-O-adenylyltransferase ANT(4')-IIb, apo

Edit deposit information
CSGID target
IDP91783 
PDB Id
4EBJ (NCBI MMDB
Authors
P.J.Stogios,Z.Wawrzak,G.Minasov,E.Evdokimova,O.Egorova,V.Yim,M.Kudritska,P.Courvalin,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Peter Stogios 
Responsible lab
University of Calgary 
Deposition Date
Mar 23, 2012 
Release Date
Apr 04, 2012 

Annotation

Description
Resistance to aminoglycoside antibiotics is mediated by chemical modifications: O-phosphorylation (APH enzymes), N-acetylation (AAC enzymes) and N-adenylation (ANT enzymes). In this entry, we present the structure of ANT(4')-IIb, an enzyme which adenylates tobramycin and amikacin antibiotics. The structure is dimeric and contains a nucleotidyltransferase domain. The antibiotic is bound in an electronegative pocket. This is only the second ANT enzyme structure and will be useful to understand the substrate discrimination mechanism and for identification of small molecule inhibitors. 
Functional assignment
nucleotidyltransferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=80.44Å, b=83.48Å, c=90.17Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.96-1.60Å (1.62-1.60Å)  
Rall(%)
16.7 
Rwork(%)
16.6 (25.1) 
Rfree(%)
19.2 (29.5) 
Num. observed reflections
81599 (2412) 
Num. Rfree reflections
4088 (122) 
Completeness(%)
96.1 (84.0) 

Model parameters

Num Atoms
4120  
Num Waters
772  
Num Hetatoms
958  
Model mean isotropic B factor
19.210Å2  
RMSD bond length
0.007Å  
RMSD bond angle
1.057°  
RMSD dihedral angle
11.282°
 
Filename uploaded
4EBJ.pdb (uploaded on Apr 06, 2012 2:06 PM)  
Inserted
Mar 26, 2012