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Structure of IDP00571

The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferasefrom Yersinia pestis CO92

Edit deposit information
CSGID target
IDP00571 
PDB Id
3GOS (NCBI MMDB
Authors
R.Zhang,N.Maltseva,K.Kwon,W.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Rong-guang Zhang 
Responsible lab
Argonne National Laboratory 
Deposition Date
Mar 19, 2009 
Release Date
May 12, 2009 

Annotation

Description
Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. In this 1.8A DapD structure from Yersinia pestis, there are three molecules form the trimer in the assymetric unit. 
Functional assignment
Tetrahydrodipicolinate N-succinyltransferase (DapD) 

Ligands

Ligand code Name Ligand type
MG

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=57.79Å, b=69.69Å, c=106.45Å
α=90.00, β=105.28, γ=90.00 
Solvent content
46.14  
Matthews coefficient
2.28  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
57.64-1.80Å (1.85-1.80Å)  
Rall(%)
23.0 
Rwork(%)
22.7 (26.7) 
Rfree(%)
27.2 (30.8) 
Num. observed reflections
74324 (5013) 
Num. Rfree reflections
3716 (263) 
Completeness(%)
98.2 (90.2) 

Model parameters

Num Atoms
6574  
Num Waters
285  
Num Hetatoms
0  
Model mean isotropic B factor
16.960Å2  
RMSD bond length
0.022Å  
RMSD bond angle
1.830°  
Filename uploaded
IDP571_2pdb.pdb (uploaded on May 04, 2009 5:52 PM)  
Inserted
May 04, 2009