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Structure of IDP90546

1.8 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase (pyrF) from Campylobacter jejuni subsp. jejuni NCTC 11168

Edit deposit information
CSGID target
IDP90546 
PDB Id
3RU6 (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,L.Shuvalova,I.Dubrovska,J.Winsor,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
May 04, 2011 
Release Date
May 18, 2011 

Annotation

Description
Orotidine monophosphate (OMP) decarboxylase catalyzes the final step in the de novo biosynthesis of uridine monophosphate. In most prokaryotes, OMP decarboxylase is a dimer of identical subunits, whereas in higher organisms, it is part of a bifunctional enzyme that also catalyzes the formation of OMP. The crystal structure of the apo-form Campylobacter jejuni orotidine 5'-monophosphate (OMP) decarboxylase was determined by molecular replacement and refined to an R-factor of 17.0% at 1.8 A resolution. There are two dimers in the asymmetric unit. Each monomer consists of a triosephosphate isomerase barrel and contains an active site that is located across one end of the barrel and near the dimer interface. Two iodide anions are bound at the active site in each of the four subunits. Surprisingly, Campylobacter jejuni and Bacillus subtilis OMP decarboxylases share only 31 % sequence identity, whereas they are very similar in structure with rmsd value of 1.7 A over 219 residues.  
Functional assignment
Lyase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 1 21 1  
Unit Cell

a=44.60Å, b=108.31Å, c=97.71Å
α=90.00, β=95.73, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.12-1.80Å (1.85-1.80Å)  
Rall(%)
17.0 
Rwork(%)
16.8 (23.5) 
Rfree(%)
20.3 (24.5) 
Num. observed reflections
83983 (6125) 
Num. Rfree reflections
4199 (300) 
Completeness(%)
98.4 (97.5) 

Model parameters

Num Atoms
7364  
Num Waters
549  
Num Hetatoms
591  
Model mean isotropic B factor
32.770Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.503°  
Filename uploaded
3RU6.pdb (uploaded on Jun 01, 2011 7:05 PM)  
Inserted
Jun 01, 2011