To see full content of that page you need the activeISee plugin.
Get the latest version from here.

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

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