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Structure of IDP00629

Epidermin biosynthesis protein EpiD from Staphylococcus aureus.

Edit deposit information
CSGID target
IDP00629 
PDB Id
3QJG (NCBI MMDB
Authors
J.Osipiuk,M.Makowska-Grzyska,K.Kwon,W.F.Anderson,A.Joachimiak,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Jerzy Osipiuk 
Responsible lab
Argonne National Laboratory 
Deposition Date
Jan 28, 2011 
Release Date
Feb 09, 2011 

Annotation

Description
Bacteria produce a wide range of antimicrobial peptides to protect themselves from competing microbes. One of such compounds is epidermin, a member of the lantibiotic family, produced and secreted by Staphylococcus species. Lantibiotics are synthesized as precursors and then modified by other proteins. Antimicrobial peptides such as epidermin exhibit highly potent biological activities, ranging from antimicrobial activity against methicillin-resistant Staphylococcus aureus (MRSA) to anticancer activity against mouse leukemia cells. The maturation of epidermin requires a series of modification reactions. EpiD protein catalyzes the first step of epidermin modifications which is the decarboxylation of the C-terminal cysteine residue and producing a reactive (Z)-enethiol intermediate. The reaction requires flavin mononucleotide (FMN) which is reduced to FMNH2. The protein belongs to a family of flavoproteins called as HFCD proteins (homo-oligomeric flavin- containing Cys-decarboxylases). The biologial assembly of EpiD is a dodecamer forming a sphere with 4 trimers placed at the vertices of a tetrahedron. EpiD is essential for epidermin biosynthesis.  
Functional assignment
Decarboxylase 

Ligands

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

Structure information

Unit cell parameters

Space Group
C 1 2 1  
Unit Cell

a=160.99Å, b=111.26Å, c=154.57Å
α=90.00, β=97.25, γ=90.00 
Solvent content
57.25  
Matthews coefficient
2.88  

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
45.90-2.04Å (2.10-2.04Å)  
Rall(%)
21.1 
Rwork(%)
20.8 (25.8) 
Rfree(%)
26.3 (35.1) 
Num. observed reflections
162164 (9025) 
Num. Rfree reflections
8108 (470) 
Completeness(%)
95.0 (71.8) 

Model parameters

Num Atoms
18797  
Num Waters
1504  
Num Hetatoms
0  
Model mean isotropic B factor
25.450Å2  
RMSD bond length
0.017Å  
RMSD bond angle
1.629°  
Filename uploaded
x08e_refmac1.pdb (uploaded on Jan 28, 2011 6:12 PM)  
Inserted
Jan 28, 2011