Structure of IDP92040

2.60 Angstrom resolution crystal structure of putative ribose 5-phosphate isomerase from Toxoplasma gondii ME49 in complex with DL-Malic acid

Edit deposit information
CSGID target
IDP92040 
PDB Id
4NML (NCBI MMDB
Authors
A.S.Halavaty,I.Dubrovska,K.Flores,D.Shanmugam,L.Shuvalova,D.Roos,J.Ruan,H.Ngo,W.F.Anderson,Center For Structural Genomics Of Infectious Diseases (Csgid) 
Responsible person
Andrei Halavaty 
Responsible lab
Northwestern University 
Deposition Date
Nov 15, 2013 
Release Date
Dec 04, 2013 

Annotation

Description
The 2.6 A resolution crystal structure of the full-length putative ribose 5-phosphate isomerase from Toxoplasma gondii ME49 in complex with DL-Malic acid was determined by single anomalous dispersion method. The protein consists of two domains. The N-terminal domain folds into a parallel 5-stranded beta-sheet, antiparallel 3-stranded beta-sheet and 5 helices. The C-terminal domain folds into an antiparallel 3-stranded beta-sheet and 4 helices. The antiparallel 3-stranded beta-sheet of the N-terminal domain is positioned at the interface of the two domains. Molecule of D-malate is bound to the protein at a surface exposed positively charged pocket located at the interface of the two domains. The PISA and crystal packing analysis revealed that the protein forms two types of dimers along two two-fold axes. One dimer has 3300 A2 and another 2400 A2 in total buried surface area. Further crystal packing analysis also revealed that protein is arranged in an octameric ring-like structure with large solvent channels (30+ Angstroms) along the four-fold axis.  
Functional assignment
Isomerase 

Ligands

Ligand code Name Ligand type
CME modified residue
CL crystallization
MLT biological
175 3,5-dihydro-5-methylidene-4h-imidazol-4-on

Structure information

Unit cell parameters

Space Group
P 41 2 2  
Unit Cell

a=95.59Å, b=95.59Å, c=112.69Å
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
29.53-2.60Å (2.67-2.60Å)  
Rall(%)
16.6 
Rwork(%)
16.4 (25.8) 
Rfree(%)
20.5 (34.4) 
Num. observed reflections
16644 (1197) 
Num. Rfree reflections
848 (63) 
Completeness(%)
99.8 (99.8) 

Model parameters

Num Atoms
1853  
Num Waters
71  
Num Hetatoms
132  
Model mean isotropic B factor
56.850Å2  
RMSD bond length
0.012Å  
RMSD bond angle
1.711°  
Filename uploaded
4NML.pdb (uploaded on Jun 05, 2015 12:10 PM)  
Inserted
Nov 22, 2013