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Structure of IDP90785

2.1 Angstrom resolution crystal structure of an orotate phosphoribosyltransferase (pyrE) from Vibrio cholerae O1 biovar eltor str. N16961

Edit deposit information
CSGID target
IDP90785 
PDB Id
3N2L (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,L.Shuvalova,I.Dubrovska,J.Winsor,K.Kwon,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
May 18, 2010 
Release Date
Jun 02, 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 Vibrio cholerae O1 biovar eltor str. N16961 has been solved and refined to 2.1 Å resolution. The asymmetric unit contains eight molecules, which pack in two tetramers (ABCD and EFGH). Total buried surface area of both oligomers is about 9500 squared Angstroms. In each tetramer two types of dimers are observed. For example, in ABCD tetramer there are AB (2670 sq. A), AC IDP90785 shares about 20 % sequence homology with IDP04423, an OPRTase from Bacillus anthracis. Pairwise structure alignment of two IDPs reveals the lowest rmsd of 2.5 Angstrom.  
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 1 21 1  
Unit Cell

a=96.59Å, b=76.71Å, c=133.94Å
α=90.00, β=92.63, γ=90.00 
Solvent content
47.78  
Matthews coefficient
2.36  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-2.10Å (2.15-2.10Å)  
Rall(%)
22.4 
Rwork(%)
22.2 (29.2) 
Rfree(%)
26.9 (32.2) 
Num. observed reflections
114000 (8257) 
Num. Rfree reflections
5700 (384) 
Completeness(%)
99.5 (98.2) 

Model parameters

Num Atoms
11785  
Num Waters
639  
Num Hetatoms
651  
Model mean isotropic B factor
44.830Å2  
RMSD bond length
0.015Å  
RMSD bond angle
1.567°  
Filename uploaded
3N2L.pdb (uploaded on Sep 17, 2010 6:16 PM)  
Inserted
May 20, 2010