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Structure of IDP90711

Crystal Structure of Dihydrodipicolinate Synthase from Campylobacter jejuni subsp. jejuni NCTC 11168

Edit deposit information
CSGID target
IDP90711 
PDB Id
3LER (NCBI MMDB
Authors
Y.Kim,M.Zhou,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 15, 2010 
Release Date
Jan 26, 2010 

Annotation

Description
Dihydrodipicolinate synthase (DHDPS), a member of lyase, catalyses the reaction converting L-aspartate 4-semialdehyde and pyruvate to (S)-2,3-dihydropyridine-2,6-dicarboxylate and water. DHDPS from C. jejuni has a TIM barrel structure like all other family proteins which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue (Lys-166) in the barrel. DHDPS is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
MCL nz-(1-carboxyethyl)-lysine biological
EDO
MG
FMT
PEG
ACY
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=72.19Å, b=85.30Å, c=199.16Å
α=90.00, β=90.00, γ=90.00 
Solvent content
46.43  
Matthews coefficient
2.3  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
39.21-1.84Å (1.91-1.84Å)  
Rall(%)
15.4 
Rwork(%)
15.2 (18.8) 
Rfree(%)
19.0 (24.0) 
Num. observed reflections
112459 (10600) 
Num. Rfree reflections
5611 (519) 
Completeness(%)
99.8 (100.0) 

Model parameters

Num Atoms
10463  
Num Waters
1100  
Num Hetatoms
0  
Model mean isotropic B factor
31.870Å2  
RMSD bond length
0.013Å  
RMSD bond angle
1.369°  
RMSD dihedral angle
19.17°
 
Filename uploaded
dep1w.pdb (uploaded on Jan 16, 2010 6:39 PM)  
Inserted
Jan 16, 2010