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Structure of IDP00520

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF from Yersinia pestis

Edit deposit information
CSGID target
IDP00520 
PDB Id
3F6M (NCBI MMDB
Authors
Y.Kim,N.Maltseva,J.Stam,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Nov 06, 2008 
Release Date
Nov 25, 2008 

Annotation

Description
2C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) synthase (MECS, EC: 4.6.1.12) is the fifth enzyme of the nonmevalonate terpenoid pathway for isopentenyl diphosphate biosynthesis and further Taxol biosynthesis. The IspF, determined by SAD to 2.96 A, is an alpha/beta structure that forms a trimer.  
Functional assignment
lyase 

Ligands

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

Structure information

Unit cell parameters

Space Group
I 21 3  
Unit Cell

a=146.64Å, b=146.64Å, c=146.64Å
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
46.37-2.96Å (3.04-2.96Å)  
Rall(%)
19.5 
Rwork(%)
19.4 (28.4) 
Rfree(%)
20.3 (29.9) 
Num. observed reflections
11092 (796) 
Num. Rfree reflections
532 (32) 
Completeness(%)
100.0 (100.0) 

Model parameters

Num Atoms
1195  
Num Waters
15  
Num Hetatoms
47  
Model mean isotropic B factor
98.510Å2  
RMSD bond length
0.016Å  
RMSD bond angle
1.555°  
Filename uploaded
3F6M.pdb (uploaded on Oct 07, 2010 5:59 PM)  
Inserted
Nov 19, 2008