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Structure of IDP90671

Pyridoxal phosphate biosynthetic protein PdxJ from Campylobacter jejuni in complex with pyridoxine-5'-phosphate.

Edit deposit information
CSGID target
IDP90671 
PDB Id
3O6D (NCBI MMDB
Authors
J.Osipiuk,M.Zhou,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jul 28, 2010 
Release Date
Aug 11, 2010 

Annotation

Description
Pyridoxal phosphate biosynthetic protein PdxJ is involved in the de novo synthesis of pyridoxal 5'-phosphate (Vitamin B6). Vitamin B6 is necessary for over 100 enzymatic reactions. It is also implicated in numerous human body functions ranging from modulation of hormone function to its recent discovery as a potent antioxidant. Its de novo biosynthesis occurs only in bacteria, fungi and plants. PdxJ protein catalyzes the condensation of 1-deoxy-D-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxal 5'-phosphate. PdxJ is a potential target for the development of new antibiotics due to its absence in mammals. 
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
PXP pyroxidine-5'-phosphate biological
PO4 PHOSPHATE ION
MSE modified residue

Structure information

Unit cell parameters

Space Group
I 4 2 2  
Unit Cell

a=90.24Å, b=90.24Å, c=156.08Å
α=90.00, β=90.00, γ=90.00 
Solvent content
54.37  
Matthews coefficient
2.7  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
32.00-1.95Å (2.00-1.95Å)  
Rall(%)
17.1 
Rwork(%)
17.0 (23.8) 
Rfree(%)
19.7 (30.4) 
Num. observed reflections
23841 (1720) 
Num. Rfree reflections
1215 (92) 
Completeness(%)
99.5 (99.7) 

Model parameters

Num Atoms
2285  
Num Waters
113  
Num Hetatoms
0  
Model mean isotropic B factor
23.930Å2  
RMSD bond length
0.019Å  
RMSD bond angle
1.594°  
Filename uploaded
idp90671_pxp.pdb (uploaded on Jul 28, 2010 8:27 PM)  
Inserted
Jul 28, 2010