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Structure of IDP04490

Phosphoribosylamine-glycine ligase from Yersinia pestis.

Edit deposit information
CSGID target
IDP04490 
PDB Id
3MJF (NCBI MMDB
Authors
J.Osipiuk,M.Zhou,L.Papazisi,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Apr 12, 2010 
Release Date
May 26, 2010 

Annotation

Description
Phosphoribosylamine-glycine ligase (also known as glycinamide ribonucleotide synthetase (GAR-syn) and PurD protein) catalyzes the second step of the de novo purine biosynthetic pathway; the conversion of phosphoribosylamine (PRA), glycine, and ATP to glycinamide ribonucleotide (GAR), ADP, and phosphate. In the reaction, the glycine is ligated to the PRA amino group in an ATP-dependent manner and provides atoms C(4), C(5) and N(7) of the purine base. The enzyme is a member of the ATP-grasp superfamily. 
Functional assignment
 

Ligands

Ligand code Name Ligand type
GOL glycerol
PGE
PEG polyethylene glycol
EDO ETHYLENE GLYCOL
BME
SO4 sulfate molecule
NA Sodium ion
MSE modified residue

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=68.64Å, b=69.15Å, c=95.17Å
α=90.00, β=90.00, γ=90.00 
Solvent content
49.73  
Matthews coefficient
2.45  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.80-1.47Å (1.51-1.47Å)  
Rall(%)
13.7 
Rwork(%)
13.5 (22.1) 
Rfree(%)
17.4 (27.7) 
Num. observed reflections
77708 (5547) 
Num. Rfree reflections
3885 (287) 
Completeness(%)
99.7 (97.1) 

Model parameters

Num Atoms
4022  
Num Waters
512  
Num Hetatoms
0  
Model mean isotropic B factor
13.690Å2  
RMSD bond length
0.018Å  
RMSD bond angle
1.740°  
Filename uploaded
idp04490.pdb (uploaded on Apr 14, 2010 12:46 PM)  
Inserted
Apr 14, 2010