Structure of IDP90246

The Crystal structure of the apo-catalytic domain of DapE protein from V.cholerea

Edit deposit information
CSGID target
IDP90246 
PDB Id
4ONW (NCBI MMDB
Authors
B.Nocek,M.Makowska-Grzyska,R.Jedrzejczak,M.Gu,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Boguslaw Nocek 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 29, 2014 
Release Date
Apr 23, 2014 

Annotation

Description
DapE is a member of the meso-diaminopimelate (mDAP)/lysine biosynthetic pathway. The amino acids mDAP and/or lysine are essential components of the peptidoglycan cell wall for Gram-negative and most Gram-positive bacteria, providing a link between polysaccharide strands. Therefore, enzymes involved in the mDAP/lysine biosynthetic pathway are all potential antibiotic targets. DapEs are dimeric metallo-enzymes (41.6 kDa/subunit) that require two atoms of zinc per mole of polypeptide for full enzymatic activity. Comparison of apo- and zinc-bound structures reveals structural differences upon metal binding.  
Functional assignment
DapE enzyme 

Ligands

Ligand code Name Ligand type
ACT acetate crystallization
BU1 crystallization
GOL crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 32 2 1  
Unit Cell

a=49.65Å, b=49.65Å, c=232.57Å
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
77.52-1.65Å (1.69-1.65Å)  
Rall(%)
15.7 
Rwork(%)
15.6 (27.0) 
Rfree(%)
18.0 (27.7) 
Num. observed reflections
41262 (2895) 
Num. Rfree reflections
2063 (161) 
Completeness(%)
99.5 (97.5) 

Model parameters

Num Atoms
2326  
Num Waters
231  
Num Hetatoms
0  
Model mean isotropic B factor
18.980Å2  
RMSD bond length
0.024Å  
RMSD bond angle
1.938°  
Filename uploaded
TLSMD32285_0728_DEPOSIT-corrected.pdb (uploaded on Jul 30, 2011 4:02 PM)  
Inserted
Jul 30, 2011