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Structure of IDP90718

Putative RNA methyltransferase from Yersinia pestis in complex with S-adenosyl-L-homocysteine.

Edit deposit information
CSGID target
IDP90718 
PDB Id
3N4K (NCBI MMDB
Authors
J.Osipiuk,N.Maltseva,S.Peterson,W.F.Anderson,A.Joachimiak 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
May 21, 2010 
Release Date
Jun 23, 2010 

Annotation

Description
Putative RNA methyltransferase (MTase) from Yersinia pestis is similar to Escherichia coli hypothetical tRNA/rRNA methyltransferase YibK and Haemophilus influenzae YibK methyltransferase. These enzymes belong to the SpoU family of MTases, a subfamily of the α/β-knot superfamily. A putative reaction of the Yersinia pestis enzyme is 2’-O-methylation of leucyl tRNA isoacceptors. 
Functional assignment
Transferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=58.72Å, b=72.28Å, c=86.82Å
α=90.00, β=90.00, γ=90.00 
Solvent content
50.52  
Matthews coefficient
2.49  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
40.50-1.76Å (1.81-1.76Å)  
Rall(%)
16.3 
Rwork(%)
16.1 (26.1) 
Rfree(%)
19.3 (31.3) 
Num. observed reflections
37295 (2642) 
Num. Rfree reflections
1864 (130) 
Completeness(%)
99.8 (97.0) 

Model parameters

Num Atoms
2960  
Num Waters
268  
Num Hetatoms
0  
Model mean isotropic B factor
15.080Å2  
RMSD bond length
0.019Å  
RMSD bond angle
1.710°  
Filename uploaded
idp90718_sah.pdb (uploaded on May 21, 2010 6:55 PM)  
Inserted
May 21, 2010