5CUX | pdb_00005cux

Crystal structure of N-terminal domain truncated Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in complex with PPi

• PDB DOI: https://doi.org/10.2210/pdb5CUX/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): Liu, W.D., Yang, Y.Y., Ko, T.P., Zheng, Y.Y., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 

Starting Model: experimental

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: 62.36 kDa 
• Atom Count: 4,434 
• Modeled Residue Count: 520 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acidocalcisomal pyrophosphatase	A, B	263	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
POP	C [auth A], D [auth A], I [auth B]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4	E [auth A], F [auth A], G [auth A], H [auth A], J [auth B], K [auth B], L [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.893	α = 90
b = 122.893	β = 90
c = 127.675	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-03-02
  Type: Initial release
  
• Version 1.1: 2016-03-09
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description