Structure of IDP91417

1.60 Angstrom resolution crystal structure of an arginine repressor from Vibrio vulnificus CMCP6

Edit deposit information
CSGID target
IDP91417 
PDB Id
3V4G (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,E.Filippova,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
Dec 14, 2011 
Release Date
Jan 04, 2012 

Annotation

Description
The 1.6 Å resolution structure of the Vibrio vulnificus arginine repressor was determined by molecular replacement using two models: (i) C-terminal domain of Escherichia coli arginine repressor/L-arginine complex (PDB code 1XXB); and (ii) the Reovirus outer capsid protein Sigma (3PDB code 1FN9). The first model was successful in finding a structure solution for a C-terminal domain of the protein, whereas the second structure was useful in finding solution for a N-terminal domain of the arginine repressor. The asymmetric unit is comprised of a single polypeptide chain with an alpha/beta fold. The N-terminal domain has three antiparallel helices and a two-stranded antiparallel β-sheet. The C-terminal domain contains a four-stranded antiparallel β-sheet and three antiparallel helices. Residues 71-76 that link the two domains are disordered in the structure. The C-terminal domain sits on a 3-fold crystallographic axis creating a trimer (buried surface area is 4380 Å2) with another two symmetry-related molecules. Another possible oligomer in the crystal is a hexamer (buried surface area is 14430 Å2) that is formed from two trimers positioned back-to-back along the aforementioned axis. 
Functional assignment
DNA BINDING PROTEIN 

Ligands

Ligand code Name Ligand type

Structure information

Unit cell parameters

Space Group
P 63 2 2  
Unit Cell

a=73.31Å, b=73.31Å, c=118.60Å
α=90.00, β=90.00, γ=120.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.65-1.60Å (1.64-1.60Å)  
Rall(%)
18.2 
Rwork(%)
18.2 (21.8) 
Rfree(%)
19.8 (27.0) 
Num. observed reflections
25557 (1828) 
Num. Rfree reflections
1303 (87) 
Completeness(%)
100.0 (100.0) 

Model parameters

Num Atoms
1257  
Num Waters
176  
Num Hetatoms
184  
Model mean isotropic B factor
23.940Å2  
RMSD bond length
0.008Å  
RMSD bond angle
1.602°  
Filename uploaded
3V4G.pdb (uploaded on Jan 10, 2012 12:27 PM)  
Inserted
Dec 26, 2011