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Structure of IDP90572

Crystal Structure of Methionyl-tRNA Formyltransferase fromYersinia pestis complexed with L-methionine

Edit deposit information
CSGID target
IDP90572 
PDB Id
3R8X (NCBI MMDB
Authors
N.Maltseva,Y.Kim,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 24, 2011 
Release Date
Apr 13, 2011 

Annotation

Description
Methionyl-tRNA(fMet) formyltransferase is important in translation initiation in prokariotes since it is responsible for the formylation of the methionyl moiety esterified to the 3' end of tRNA. It transfers 10-formyltetrahydrofolate to the L-methionyl-tRNA(fMet) which results in production of tetrahydrofolate and N-formylmethionyl-tRNA(fMet). Inactivation of this gene in Escherichia coli severely impairs growth of bacteria. Crystal Structure of Methionyl-tRNA Formyltransferase from Yersinia pestis complexed with L-methionine was solved at 2.26A resolution. The enzyme is composed of two domains (N-terminal 1-204 and C-terminal 213-314 ) with a short linker 205- 212 between them. Residues from 41 to 46 are disordered in the structure. L –methionine is situated in the N-terminal part of the protein in a cavity and coordinated by Asn109, His111, Gly120 and Asp147. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
EMM [methyl(vinyl)amino]methanol crystallization
TRS Tris(hydroxymethyl)aminomethane crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 43 2 2  
Unit Cell

a=62.75Å, b=62.75Å, c=172.64Å
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
42.97-2.26Å (2.29-2.25Å)  
Rall(%)
18.0 
Rwork(%)
17.7 (21.8) 
Rfree(%)
23.1 (29.1) 
Num. observed reflections
17851 (2737) 
Num. Rfree reflections
901 (141) 
Completeness(%)
99.6 (99.0) 

Model parameters

Num Atoms
2474  
Num Waters
142  
Num Hetatoms
165  
Model mean isotropic B factor
35.870Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.395°  
RMSD dihedral angle
15.44°
 
Filename uploaded
dep2.pdb (uploaded on Mar 24, 2011 3:35 PM)  
Inserted
Mar 24, 2011