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Structure of IDP04345

Crystal Structure of Uridine Phosphorylase from Vibrio cholerae Complexed with Uracil

Edit deposit information
CSGID target
IDP04345 
PDB Id
3PNS (NCBI MMDB
Authors
N.Maltseva,Y.Kim,J.Hasseman,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Natalia Maltseva 
Responsible lab
Argonne National Laboratory 
Deposition Date
Nov 19, 2010 
Release Date
Dec 15, 2010 

Annotation

Description
Uridine phosphorylase is an enzyme which participates in pyrimidine metabolism and belongs to the family of glycosyltransferases. It catalyzes the reversible phosphorolysis of uridine with the formation of alpha-D-ribose-1-phosphate and uracil. Crystal structure of uridine phosphorylase from Vibrio cholerae O1 biovar El Tor complexed with uracil was solved at 2.0 A resolution.  
Functional assignment
 

Ligands

Ligand code Name Ligand type
GOL crystallization
CL crystallization
SO4 crystallization
FMT crystallization
ACY crystallization
MSE modified residue
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on biological

Structure information

Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=103.28Å, b=174.46Å, c=180.02Å
α=90.00, β=90.00, γ=90.00 
Solvent content
48.07  
Matthews coefficient
2.37  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
49.64-2.00Å (2.07-2.00Å)  
Rall(%)
17.7 
Rwork(%)
17.4 (24.3) 
Rfree(%)
22.6 (30.9) 
Num. observed reflections
210895 (17251) 
Num. Rfree reflections
10586 (868) 
Completeness(%)
92.0 (80.0) 

Model parameters

Num Atoms
22969  
Num Waters
2009  
Num Hetatoms
2246  
Model mean isotropic B factor
26.660Å2  
RMSD bond length
0.011Å  
RMSD bond angle
1.277°  
RMSD dihedral angle
13.74°
 
Filename uploaded
dep.pdb (uploaded on Dec 17, 2010 2:13 PM)  
Inserted
Dec 17, 2010