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Structure of IDP01970

Crystal Structure of Isopentenyl-Diphosphate delta-Isomerase from Salmonella entericase

Edit deposit information
CSGID target
IDP01970 
PDB Id
3HYQ (NCBI MMDB
Authors
Y.Kim,M.Zhou,S.Peterson,W.F.Anderson,A.Joachimiak 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jun 22, 2009 
Release Date
Jun 30, 2009 

Annotation

Description
This enzyme catalyzes to convert isopentenyl diphosphate to its isomer dimethylallyl diphosphate as a part of mevalonate pathway which present in all higher eukaryotes and many bacteria. The protein folds into a globular α/β protein consisting of a six-stranded twisted β-sheet surrounded by four small α-helices. 
Functional assignment
 

Ligands

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

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=81.44Å, b=64.15Å, c=35.19Å
α=90.00, β=101.36, γ=90.00 
Solvent content
41.96  
Matthews coefficient
2.12  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
25.01-1.53Å (1.59-1.53Å)  
Rall(%)
16.4 
Rwork(%)
16.3 (22.7) 
Rfree(%)
18.7 (25.4) 
Num. observed reflections
27766 (2420) 
Num. Rfree reflections
1396 (125) 
Completeness(%)
97.7 (82.0) 

Model parameters

Num Atoms
1628  
Num Waters
227  
Num Hetatoms
0  
Model mean isotropic B factor
29.070Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.536°  
RMSD dihedral angle
17.8°
 
Filename uploaded
dep1w.pdb (uploaded on Jun 23, 2009 7:56 AM)  
Inserted
Jun 23, 2009