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Structure of IDP00439

Crystal Structure of Pyridoxal Phosphate Biosynthetic Protein PdxJ from Yersinia pestis

Edit deposit information
CSGID target
IDP00439 
PDB Id
3F4N (NCBI MMDB
Authors
'Y.Kim,N.Maltseva,J.Stam,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid)' 
Responsible person
Youngchang Kim 
Responsible lab
Argonne National Laboratory 
Deposition Date
Nov 01, 2008 
Release Date
Nov 25, 2008 

Annotation

Description
Pyridoxine 5`-phosphate synthase from  Yersinia pestis belongs to PdxJ family that catalyses the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate. The protein crystallized in the presence of pyridoxal 5’-phosphate (PLP) and formed an octamer of TIM-barrels with each 246 amino acid TIM barrel containing one PLP inside of the barrel. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
PXP pyroxidine-5'-phosphate biological
SO4 sulfate

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=113.63Å, b=114.82Å, c=154.32Å
α=90.00, β=90.00, γ=90.00 
Solvent content
47.99  
Matthews coefficient
2.36  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
34.81-2.40Å (2.46-2.40Å)  
Rall(%)
19.5 
Rwork(%)
19.1 (27.2) 
Rfree(%)
26.6 (42.8) 
Num. observed reflections
74939 (4944) 
Num. Rfree reflections
3746 (240) 
Completeness(%)
94.6 (86.2) 

Model parameters

Num Atoms
14781  
Num Waters
667  
Num Hetatoms
810  
Model mean isotropic B factor
23.630Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.792°  
Filename uploaded
rcsb050141.pdb (uploaded on Dec 01, 2008 1:10 PM)  
Inserted
Dec 01, 2008