Structure of IDP91458

Type II citrate synthase from Vibrio vulnificus.

Edit deposit information
CSGID target
IDP91458 
PDB Id
4E6Y (NCBI MMDB
Authors
J.Osipiuk,M.Gu,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
Mar 16, 2012 
Release Date
Mar 28, 2012 

Annotation

Description
Citrate synthases catalyze the first reaction in the citric acid cycle (the Krebs' cycle), namely the condensation of acetyl-coenzyme A with oxaloacetate to form citrate and coenzyme A. This reaction is important for energy generation and for carbon assimilation. The enzymes are found in two distinct structural types: type I enzymes (found in eukaryotes, Gram-positive bacteria and Archaea) forming homodimers and type II enzymes, which are found in Gram-negative bacteria and are hexameric in structure. The enzyme monomer is composed of two alpha-helical domains. The cleft between these domains forms the active site. Type II enzymes possess an extra N-terminal beta-sheet domain. 
Functional assignment
transferase 

Ligands

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

Structure information

Unit cell parameters

Space Group
P 63 2 2  
Unit Cell

a=109.72Å, b=109.72Å, c=153.65Å
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
95.02-2.50Å (2.56-2.50Å)  
Rall(%)
19.1 
Rwork(%)
18.9 (25.3) 
Rfree(%)
23.1 (34.4) 
Num. observed reflections
19512 (1239) 
Num. Rfree reflections
995 (60) 
Completeness(%)
99.6 (99.6) 

Model parameters

Num Atoms
3433  
Num Waters
50  
Num Hetatoms
0  
Model mean isotropic B factor
52.480Å2  
RMSD bond length
0.014Å  
RMSD bond angle
1.673°  
Filename uploaded
idp91458.pdb (uploaded on Mar 16, 2012 12:01 PM)  
Inserted
Mar 16, 2012