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Structure of IDP00331

Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase from Francisella tularensis

Edit deposit information
CSGID target
IDP00331 
PDB Id
3RE3 (NCBI MMDB
Authors
Y.Kim,M.Makowska-Grzyska,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Apr 02, 2011 
Release Date
Apr 27, 2011 

Annotation

Description
This enzyme IspF is a part of isoprenoid precursor biosynthesis and catalyzes the reaction synthesizing 2-C-methyl-D-erythritol 2,4-cyclodiphosphate from 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. As isoprenoid precursor biosynthesis occurs in many pathogens while it is absent in human, IspF has been an attractive drug target. This alpha-beta trimeric structure formed by sharing the hydrophobic sides of each of an beta sheet. An pyrophosphate molecule, co-crystalized with the protein, was found in the patch located at the bottom of each protein chain.  
Functional assignment
Lyase 

Ligands

Ligand code Name Ligand type
CL crystallization
MPD crystallization
NA Sodium ion crystallization
POP pyrophosphate 2- crystallization
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 63  
Unit Cell

a=96.12Å, b=96.12Å, c=155.31Å
α=90.00, β=90.00, γ=120.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
41.62-2.65Å (2.75-2.65Å)  
Rall(%)
17.6 
Rwork(%)
17.3 (28.7) 
Rfree(%)
22.7 (37.0) 
Num. observed reflections
24740 (2528) 
Num. Rfree reflections
1274 (126) 
Completeness(%)
99.1 (96.0) 

Model parameters

Num Atoms
4655  
Num Waters
63  
Num Hetatoms
117  
Model mean isotropic B factor
72.870Å2  
RMSD bond length
0.008Å  
RMSD bond angle
1.144°  
RMSD dihedral angle
16.208°
 
Filename uploaded
dep.pdb (uploaded on Apr 02, 2011 11:48 AM)  
Inserted
Apr 02, 2011