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Structure of IDP00067

2.7 Angstrom resolution crystal structure of a probable holliday junction DNA helicasae (ruvB) from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with adenosine-5'-diphospahte

Edit deposit information
CSGID target
IDP00067 
PDB Id
3PFI (NCBI MMDB
Authors
A.S.Halavaty,Z.Wawrzak,T.Skarina,O.Onopriyenko,A.Edwards,A.Savchenko,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Oct 28, 2010 
Release Date
Nov 10, 2010 

Annotation

Description
The structure of the putative Se-Met holliday junction DNA helicase (ruvB) from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with ADP was solved by SAD. There are two copies of the protein in the H32 space group’s asymmetric unit, which form a dimer with the buried surface area of ~2700 A2. Single chain of the putative helicase consists of three distinct domains and binds one copy of ADP molecule. All three domains are involved in dimerization. Examining the crystal packing, it can be seen that protein forms a hexamer with the buried surface area of 16460 A2 and having ~22 A wide channel in the middle of the oligomer.  
Functional assignment
HYDROLASE 

Ligands

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

Structure information

Unit cell parameters

Space Group
H 3 2  
Unit Cell

a=111.48Å, b=111.48Å, c=355.09Å
α=90.00, β=90.00, γ=120.00 
Solvent content
56.02  
Matthews coefficient
2.8  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.59-2.69Å (2.77-2.69Å)  
Rall(%)
22.4 
Rwork(%)
22.2 (32.9) 
Rfree(%)
26.8 (40.8) 
Num. observed reflections
23883 (1686) 
Num. Rfree reflections
1241 (95) 
Completeness(%)
99.8 (98.0) 

Model parameters

Num Atoms
4454  
Num Waters
31  
Num Hetatoms
182  
Model mean isotropic B factor
67.630Å2  
RMSD bond length
0.005Å  
RMSD bond angle
1.033°  
Filename uploaded
3PFI.pdb (uploaded on Sep 28, 2011 11:15 AM)  
Inserted
Nov 01, 2010