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Structure of IDP01970

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

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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

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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

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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