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Structure of IDP04423

1.75 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase from Bacillus anthracis str. 'Ames Ancestor'

Edit deposit information
CSGID target
IDP04423 
PDB Id
3M3H (NCBI MMDB
Authors
A.S.Halavaty,L.Shuvalova,G.Minasov,J.Winsor,I.Dubrovska,K.Kwon,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Mar 09, 2010 
Release Date
Apr 14, 2010 

Annotation

Description
Orotate phosphoribosyltransferase (OPRTase) is involved in the de novo biosynthesis of pyrimidine nucleotides by catalyzing the Mg2+ dependent formation of orotidine 5‘-monophosphate (OMP), from which uridine 5‘-monophosphate is synthesized. Crystal structure of OPRTase from Bacillus anthracis str. 'Ames Ancestor' has been solved and refined to 1.75 Å resolution with a single copy of the protein per asymmetric unit. The structure resembles the structure of the OPRTase from Streptococcus mutans, which was used as a molecular replacement model. Crystal packing reveals that the B. anthracis OPRTase is a homodimer with a total buried surface area of 1950 Å. In the dimer, active site of each chain is at oligomerization interface. The residues Thr71 through Gly75 and Arg94 through Asn104 are structurally disordered.  
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 41 21 2  
Unit Cell

a=56.76Å, b=56.76Å, c=113.71Å
α=90.00, β=90.00, γ=90.00 
Solvent content
31.5  
Matthews coefficient
1.8  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.43-1.75Å (1.80-1.75Å)  
Rall(%)
18.1 
Rwork(%)
17.9 (18.2) 
Rfree(%)
22.3 (24.1) 
Num. observed reflections
19350 (1400) 
Num. Rfree reflections
986 (79) 
Completeness(%)
99.4 (100.0) 

Model parameters

Num Atoms
1642  
Num Waters
110  
Num Hetatoms
119  
Model mean isotropic B factor
19.590Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.280°  
Filename uploaded
3M3H.pdb (uploaded on Sep 17, 2010 7:06 PM)  
Inserted
Apr 05, 2010