Structure of IDP92645

1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655

Edit deposit information
CSGID target
IDP92645 
PDB Id
4QUS (NCBI MMDB
Authors
A.S.Halavaty,E.V.Filippova,G.Minasov,K.J.Flores,I.Dubrovska,L.Shuvalova,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Jul 11, 2014 
Release Date
Jul 23, 2014 

Annotation

Description
The 1.28 A resolution crystal structure of acyl-CoA N-acyltransferase domain (ypeA) of putative acyltransferase from Escherichia coli str. K-12 substr. MG1655 was determined by molecular replacement. There are two similar in the tertiary structure (0.8 A r.ms.d. over 139 C-alpha atoms) copies of the protein within the I4 asymmetric unit that form a dimer (5800 A2). 38 hydrogen-bonded and 333 van der Waals contacts hold the dimer together. Crystal packing demonstrates that the domain may form octamers (32700 A2) too. The acyl-CoA N-acyltransferase domain is organized into a compact core subdomain with an antiparallel 4-stranded beta-sheet that is flanked by 4 helices. Additional strand-helix-strand structural motif represents a dimerization subdomain domain. There is an extended solvent-exposed groove between the dimerization and core domain that serves as a docking site for acyl-CoA molecule co-crystallized with the acyl-CoA N-acyltransferase domain (ypeA) (see Annotation for the PDB entry 4qvt).  
Functional assignment
Transferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
I 4  
Unit Cell

a=90.82Å, b=90.82Å, c=84.17Å
α=90.00, β=90.00, γ=90.00 
Solvent content
 
Matthews coefficient
 

Refinement

Data for the highest resolution shell is in parentheses.
Resolution range
28.72-1.28Å (1.31-1.28Å)  
Rall(%)
11.1 
Rwork(%)
10.9 (19.0) 
Rfree(%)
13.9 (23.4) 
Num. observed reflections
87232 (6328) 
Num. Rfree reflections
4361 (314) 
Completeness(%)
99.7 (98.5) 

Model parameters

Num Atoms
2528  
Num Waters
537  
Num Hetatoms
573  
Model mean isotropic B factor
20.900Å2  
RMSD bond length
0.010Å  
RMSD bond angle
1.643°  
Filename uploaded
4QUS.pdb (uploaded on Jul 24, 2014 12:33 PM)  
Inserted
Jul 24, 2014