Structure of IDP91189

Crystal structure of aminoglycoside phosphotransferase APH(2")-Id/APH(2")-IVa in complex with HEPES

Edit deposit information
CSGID target
IDP91189 
PDB Id
4DE4 (NCBI MMDB
Authors
P.J Stogios,G.Minasov,K.Tan,B.Nocek,E.Evdokimova,O.Egorova,R.Di Leo,H.Li,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Peter Stogios 
Responsible lab
University of Calgary 
Deposition Date
Jan 19, 2012 
Release Date
Feb 08, 2012 

Annotation

Description
Aminoglycoside phosphotransferase (APH) enzymes act in a substrate- and position-specific manner and confer resistance to the activity of various aminoglycoside antibiotics. APH enzymes show a eukaryotic protein kinase-like fold with an insertion that takes part in substrate recognition. This is the gentamicin-bound structure of APH(2'')-Id/APH(2'')-IVa, an enzyme that acts on gentamicin and kanamycin. 
Functional assignment
kinase 

Ligands

Ligand code Name Ligand type
EPE crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=42.54Å, b=101.21Å, c=71.17Å
α=90.00, β=97.51, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.99-2.00Å (2.07-2.00Å)  
Rall(%)
22.4 
Rwork(%)
22.2 (31.8) 
Rfree(%)
27.2 (36.0) 
Num. observed reflections
40668 (3668) 
Num. Rfree reflections
2102 (190) 
Completeness(%)
95.9 (92.0) 

Model parameters

Num Atoms
4799  
Num Waters
270  
Num Hetatoms
439  
Model mean isotropic B factor
48.430Å2  
RMSD bond length
0.002Å  
RMSD bond angle
0.599°  
RMSD dihedral angle
11.448°
 
Filename uploaded
4DE4.pdb (uploaded on Feb 14, 2012 9:26 AM)  
Inserted
Mar 23, 2011