5UPR | pdb_00005upr

X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49

• PDB DOI: https://doi.org/10.2210/pdb5UPR/pdb

• Classification: ISOMERASE
• Organism(s): Toxoplasma gondii ME49
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-02-03 Released: 2017-02-22 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Cardona-Correa, A., Bishop, B., Anderson, W.F., Ngo, H., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Literature

X-ray structure of a putative triosephosphate isomerase from Toxoplasma gondii ME49

Filippova, E.V., Wawrzak, Z., Minasov, G., Cardona-Correa, A., Bishop, B., Anderson, W.F., Ngo, H., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 114.22 kDa 
• Atom Count: 8,876 
• Modeled Residue Count: 1,033 
• Deposited Residue Count: 1,060 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, C, D	265	Toxoplasma gondii ME49	Mutation(s): 0  Gene Names: TPI-II, TGME49_233500 EC: 5.3.1.1
UniProt
Find proteins for A0A125YP67 (Toxoplasma gondii (strain ATCC 50611 / Me49)) Explore A0A125YP67  Go to UniProtKB:  A0A125YP67

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], F [auth A], H [auth B], J [auth C], L [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	G [auth A], I [auth B], K [auth C], M [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35upr

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.368	α = 90
b = 115.533	β = 90.02
c = 78.719	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Cardona-Correa, A., Bishop, B., Anderson, W.F., Ngo, H., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-07-19
  Changes: Database references, Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Refinement description, Structure summary