4JEP | pdb_00004jep

Crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 (NTPDase1)

• PDB DOI: https://doi.org/10.2210/pdb4JEP/pdb

• Classification: HYDROLASE
• Organism(s): Toxoplasma gondii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-02-27 Released: 2013-04-10 
• Deposition Author(s): Krug, U., Totzauer, R., Strater, N.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.305 (Depositor), 0.344 (DCC) 
• R-Value Work: 
  0.270 (Depositor), 0.303 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Literature

The crystal structure of Toxoplasma gondii nucleoside triphosphate diphosphohydrolase 1 represents a conformational intermediate in the reductive activation mechanism of the tetrameric enzyme.

Krug, U., Totzauer, R., Strater, N.

(2013) Proteins 81: 1271-1276

• PubMed: 23526564 
• DOI: https://doi.org/10.1002/prot.24288
• Primary Citation Related Structures: 
  4JEP


• PubMed Abstract: 
  

  Toxoplasma gondii nucleoside triphosphate diphosphohydrolase (NTPDase) 1 was crystallized in an intermediate tetrameric conformation. The crystal structure is similar to that of T. gondii NTPDase3 and represents an inactive conformation as the activating disulfide bridge is not reduced and the active site cleft between the two domains of each monomer is open. However, the arrangement of the monomers within the tetramer differs from that of the inactive form of NTPDase3 and may represent an intermediate conformation on the path of the closure motion of the tetramer induced upon activation.

---

Organizational Affiliation: 
• Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Center for Biotechnology and Biomedicine, University of Leipzig, 04103 Leipzig, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 136.15 kDa 
• Atom Count: 8,772 
• Modeled Residue Count: 1,126 
• Deposited Residue Count: 1,222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside-triphosphatase 2	A, B	611	Toxoplasma gondii	Mutation(s): 0  Gene Names: NTP1 EC: 3.6.1.15
UniProt
Find proteins for Q27895 (Toxoplasma gondii) Explore Q27895  Go to UniProtKB:  Q27895

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.305 (Depositor), 0.344 (DCC) 
• R-Value Work:  0.270 (Depositor), 0.303 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.743	α = 90
b = 161.517	β = 90
c = 236.937	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Krug, U., Totzauer, R., Strater, N.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release
  
• Version 1.1: 2013-07-10
  Changes: Database references
• Version 1.2: 2013-12-25
  Changes: Structure summary
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary