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Structure of IDP90611

2.25 Angstrom resolution crystal structure of a thymidylate kinase (tmk) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with thymidine

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CSGID target
IDP90611 
PDB Id
3N2I (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
May 18, 2010 
Release Date
Jun 02, 2010 

Annotation

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Description
A thymidylate kinase catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP). This enzyme from Vibrio cholerae O1 biovar eltor str. N16961 was co-crystallized with thymidine. Crystal diffracted to 2.25 Å resolution and a molecular replacement solution was obtained using the structure of the Vibrio cholerae O1 biovar eltor str. N16961 thymidylate kinase (PDB ID 3LV8).  
Functional assignment
Transferase 

Ligands

Ligand code Name Ligand type
THM thymidine biological
CL chloride

Structure information

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Unit cell parameters

Space Group
I 41 2 2  
Unit Cell

a=92.60Å, b=92.60Å, c=231.54Å
α=90.00, β=90.00, γ=90.00 
Solvent content
47.58  
Matthews coefficient
2.35  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.64-2.25Å (2.31-2.25Å)  
Rall(%)
20.8 
Rwork(%)
20.6 (28.9) 
Rfree(%)
26.1 (28.6) 
Num. observed reflections
24313 (1739) 
Num. Rfree reflections
1239 (86) 
Completeness(%)
99.9 (99.8) 

Model parameters

Num Atoms
3258  
Num Waters
77  
Num Hetatoms
113  
Model mean isotropic B factor
69.840Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.844°  
Filename uploaded
3N2I.pdb (uploaded on Sep 17, 2010 5:56 PM)  
Inserted
May 21, 2010