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Structure of IDP02311

1.9 Angstrom Crystal Structure of Orotate Phosphoribosyltransferase (pyrE) Francisella tularensis.

Edit deposit information
CSGID target
IDP02311 
PDB Id
3MJD (NCBI MMDB
Authors
G.Minasov,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
George Minasov 
Responsible lab
Northwestern University 
Deposition Date
Apr 12, 2010 
Release Date
Apr 21, 2010 

Annotation

Description
Orotate phosphoribosyltransferase (OPRTase) is involved in the biosynthesis of pyrimidine nucleotides. Alpha-D-ribosyldiphosphate 5-phosphate (PRPP) and orotate are utilized to form pyrophosphate and orotidine 5'-monophosphate (OMP) in the presence of divalent cations, preferably Mg2+. OMP is thereafter converted to uridine 5'-monophosphate by OMP decarboxylase. We have determined the 1.9 angstrom structure of Francisella tularensis subsp. tularensis SCHU S4 OPRTase (PyrE). The OPRTase three-dimensional structure reveals two major features: a core five-stranded alpha/beta twisted sheet and an N-terminal region that partially covers the C-terminal portion of the core. PRTases show a very high degree of base specificity. 
Functional assignment
Purines, pyrimidines, nucleosides, and nucleotides; subcategory: Pyrimidine ribonucleotide biosynthesis 

Ligands

Ligand code Name Ligand type
TRS Tris(hydroxymethyl)aminomethane crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=82.55Å, b=97.90Å, c=110.72Å
α=90.00, β=90.00, γ=90.00 
Solvent content
42.57  
Matthews coefficient
2.14  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.47-1.90Å (1.95-1.90Å)  
Rall(%)
18.8 
Rwork(%)
18.6 (22.0) 
Rfree(%)
23.5 (28.1) 
Num. observed reflections
71312 (5209) 
Num. Rfree reflections
3636 (263) 
Completeness(%)
100.0 (99.9) 

Model parameters

Num Atoms
6829  
Num Waters
692  
Num Hetatoms
710  
Model mean isotropic B factor
24.670Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.241°  
Filename uploaded
rcsb058617.pdb (uploaded on Apr 16, 2010 4:51 PM)  
Inserted
Apr 16, 2010