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Structure of IDP91779

Crystal structure of lincosamide antibiotic adenylyltransferase LnuA, lincomycin-bound

Edit deposit information
CSGID target
IDP91779 
PDB Id
4E8J (NCBI MMDB
Authors
P.J.Stogios,A.Dong,G.Minasov,E.Evdokimova,O.Egorova,M.Kudritska,V.Yim,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 20, 2012 
Release Date
Apr 04, 2012 

Annotation

Description
One mechanism of resistance to the antibiotic lincomycin, a compound that is used to treat numerous infections, is conferred by adenylation by enzymes of the lin family. In this entry, we demonstrate the structure of LinA in the apo and lincomycin-bound forms. The enzyme adopts a structure similar to LinB (PDB 3JZO), but also shows some novel features including an insertion of approximately six residues in the active site, and a novel dimerization mechanism. 
Functional assignment
nucleotidyltransferase 

Ligands

Ligand code Name Ligand type
CL chloride crystallization
LN0 biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=56.45Å, b=63.44Å, c=60.81Å
α=90.00, β=101.60, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
23.35-1.82Å (1.87-1.82Å)  
Rall(%)
19.8 
Rwork(%)
19.6 (31.0) 
Rfree(%)
23.4 (35.9) 
Num. observed reflections
39667 (2427) 
Num. Rfree reflections
2102 (141) 
Completeness(%)
99.6 (97.0) 

Model parameters

Num Atoms
2618  
Num Waters
419  
Num Hetatoms
534  
Model mean isotropic B factor
26.080Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.378°  
RMSD dihedral angle
15.744°
 
Filename uploaded
4E8J.pdb (uploaded on Apr 30, 2014 9:00 AM)  
Inserted
Mar 26, 2012