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Structure of IDP90525

1.77 Angstrom resolution crystal structure of orotidine 5'-phosphate decarboxylase from Vibrio cholerae O1 biovar eltor str. N16961

Edit deposit information
CSGID target
IDP90525 
PDB Id
3LDV (NCBI MMDB
Authors
A.S.Halavaty,L.Shuvalova,G.Minasov,I.Dubrovska,J.Winsor,E.M.Glass,S.N.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jan 13, 2010 
Release Date
Jan 26, 2010 

Annotation

Description
Orotidine 5′-monophosphate decarboxylase catalyses the decarboxylation of orotidine 5′-monophosphate to uridine 5′-monophosphate (UMP) without the aid of any metal ions or cofactors. This reaction is the last step in the de novo synthesis of pyrimidine nucleotides. We have determined an apo-structure of orotidine 5′-monophosphate decarboxylase from Vibrio cholerae. Two chains of the protein in the asymmetric unit form a closely bound homodimer. Each subunit of the dimer folds as an alpha/beta-barrel with eight central beta-strands flanked by eleven alpha helices. There is one active sites per subunit located at the C termini of the beta-strands of the barrel. Residues from both chains contribute to formation of each active site. A conserved unique motif Lys-Asp-Lys-Asp of the active site is present in the V. cholerae decarboxylase. Structures of binary complexes with UMP and known inhibitor 1-(5′-phospho-beta-D-ribofuranosyl)barbituric acid (BMP) can help to elucidate the mechanism of the reaction catalyzed by the protein.  
Functional assignment
Lyase 

Ligands

Ligand code Name Ligand type
MG
CL CHLORIDE ION

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=47.30Å, b=94.67Å, c=99.18Å
α=90.00, β=90.00, γ=90.00 
Solvent content
38.46  
Matthews coefficient
2  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
30.00-1.77Å (1.82-1.77Å)  
Rall(%)
15.5 
Rwork(%)
15.4 (22.9) 
Rfree(%)
18.5 (26.2) 
Num. observed reflections
43729 (3076) 
Num. Rfree reflections
2186 (164) 
Completeness(%)
99.4 (95.8) 

Model parameters

Num Atoms
3637  
Num Waters
593  
Num Hetatoms
608  
Model mean isotropic B factor
29.090Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.383°  
Filename uploaded
3LDV.pdb (uploaded on Sep 17, 2010 5:41 PM)  
Inserted
Jan 14, 2010