Structure of IDP91783

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

Edit deposit information
CSGID target
IDP91783 
PDB Id
4EBK (NCBI MMDB
Authors
P.J.Stogios,A.Dong,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
IOD iodide ion crystallization
EDO crystallization
TOY tobramycin biological
MSE modified residue
IYR 3-iodo-tyrosine 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=81.91Å, b=84.45Å, c=98.76Å
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
23.89-2.15Å (2.17-2.15Å)  
Rall(%)
17.4 
Rwork(%)
17.2 (25.5) 
Rfree(%)
22.1 (35.0) 
Num. observed reflections
39914 (2355) 
Num. Rfree reflections
2111 (130) 
Completeness(%)
99.5 (87.0) 

Model parameters

Num Atoms
4042  
Num Waters
475  
Num Hetatoms
686  
Model mean isotropic B factor
38.600Å2  
RMSD bond length
0.008Å  
RMSD bond angle
1.142°  
RMSD dihedral angle
13.155°
 
Filename uploaded
4EBK.pdb (uploaded on Apr 06, 2012 2:03 PM)  
Inserted
Mar 29, 2012