5CUV | pdb_00005cuv

Crystal structure of Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in apo form

• PDB DOI: https://doi.org/10.2210/pdb5CUV/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Trypanosoma cruzi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-25 Released: 2016-03-02 
• Deposition Author(s): Ko, T.P., Yang, Y.Y., Liu, W.D., Zheng, Y.Y., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.235 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.189 (DCC) 

Literature

Crystal structure of Trypanosoma cruzi protein in complex with ligand

Yang, Y.Y., Ko, T.P., Zheng, Y.Y., Liu, W.D., Chen, C.C., Guo, R.T.

(2016) ACS Chem Biol 

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: 97.89 kDa 
• Atom Count: 6,578 
• Modeled Residue Count: 761 
• Deposited Residue Count: 828 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acidocalcisomal pyrophosphatase	A, B	414	Trypanosoma cruzi	Mutation(s): 0  EC: 3.6.1.1
UniProt
Find proteins for Q4JH30 (Trypanosoma cruzi) Explore Q4JH30  Go to UniProtKB:  Q4JH30

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLT	C [auth A]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N
MG	D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.235 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.189 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.518	α = 90
b = 103.017	β = 90
c = 157.398	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-02 
Deposition Author(s): Ko, T.P., Yang, Y.Y., Liu, W.D., Zheng, Y.Y., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary