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 | chloride | 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
- 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)
- 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