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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 
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
PGE
PEG
EDO
BME
SO4
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