Structure of IDP91387

1.80 Angstrom resolution crystal structure of a putative translation initiation inhibitor from Vibrio vulnificus CMCP6

Edit deposit information
CSGID target
IDP91387 
PDB Id
3VCZ (NCBI MMDB
Authors
A.S.Halavaty,G.Minasov,E.V.Filippova,I.Dubrovska,J.Winsor,L.Shuvalova,L.Papazisi,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jan 04, 2012 
Release Date
Jan 25, 2012 

Annotation

Description
The X-ray structure of a putative translation initiation inhibitor from Vibrio vulnificus CMCP6 was determined by molecular replacement and refined to 1.8 Å resolution. Asymmetric unit is comprised of three identical chains that form a trimer with buried surface area of 7,410 Å2. Every polypeptide chain possesses six-stranded antiparallel β-sheet that faces the interior of the trimer creating a β-barrel. Five α-helices and adjacent loops flank the β-sheet. The protein has a β3,α2, β,α2,β,α,β topology. The interior of the barrel has two hydrophobic sections that are on the terminal opposite sides of the structure and one hydrophilic section that has trapped water molecules.  
Functional assignment
Translation 

Ligands

Ligand code Name Ligand type
MG crystallization
CA crystallization
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=71.88Å, b=86.58Å, c=68.16Å
α=90.00, β=90.67, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
29.13-1.80Å (1.85-1.80Å)  
Rall(%)
15.7 
Rwork(%)
15.5 (23.7) 
Rfree(%)
18.3 (26.6) 
Num. observed reflections
38399 (2587) 
Num. Rfree reflections
1919 (139) 
Completeness(%)
99.3 (91.2) 

Model parameters

Num Atoms
3038  
Num Waters
314  
Num Hetatoms
388  
Model mean isotropic B factor
21.680Å2  
RMSD bond length
0.008Å  
RMSD bond angle
1.487°  
Filename uploaded
3VCZ.pdb (uploaded on Mar 15, 2012 1:12 PM)  
Inserted
Jan 10, 2012