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Structure of IDP01880

1.75 Angstrom resolution crystal structure of a putative NTP pyrophosphohydrolase (yfaO) from Salmonella typhimurium LT2

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CSGID target
IDP01880 
PDB Id
3OGA (NCBI MMDB) 
Authors
A.S.Halavaty,G.Minasov,L.Shuvalova,J.Winsor,I.Dubrovska,S.Peterson,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Aug 16, 2010 
Release Date
Oct 06, 2010 

Annotation

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Description
The 1.75 A resolution structure of the wild type IDP01880 protein was solved by molecular replacement using the structure of this protein (PDB ID 3N77) with three point mutations (K118A, E120A, E121A) as a model. It is interesting to note that both structures have different crystal packing, which might be a result of site-directed mutagenesis. Pairwise structural alignment clearly shows that the residues Lys188, Glu120 and Glu121 if not mutated would clash with the Leu63-Ile66 stretch of residues of symmetry related molecule in the 3N77 structure. Residues 25 through 30 in chain A of the 3OGA structure are disordered, whereas they are built in chain B. These residues constitute a loop, which conformation is different from that of the mutant structure. Additionally, residues 78 through 88 in chain B and residues 82-83 in chain A of the wild type structure are disordered.  
Functional assignment
Hydrolase 

Ligands

Ligand code Name Ligand type
PO4 biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

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Unit cell parameters

Space Group
P 21 21 21  
Unit Cell

a=41.59Å, b=81.10Å, c=110.08Å
α=90.00, β=90.00, γ=90.00 
Solvent content
49.48  
Matthews coefficient
2.43  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.03-1.75Å (1.80-1.75Å)  
Rall(%)
18.7 
Rwork(%)
18.5 (21.7) 
Rfree(%)
21.8 (24.9) 
Num. observed reflections
38165 (2700) 
Num. Rfree reflections
1908 (141) 
Completeness(%)
99.5 (96.9) 

Model parameters

Num Atoms
2292  
Num Waters
237  
Num Hetatoms
291  
Model mean isotropic B factor
37.450Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.502°  
Filename uploaded
3OGA.pdb (uploaded on Sep 28, 2011 11:24 AM)  
Inserted
Aug 18, 2010