5CUY | pdb_00005cuy

Crystal structure of Trypanosoma brucei Vacuolar Soluble Pyrophosphatases in apo form

• PDB DOI: https://doi.org/10.2210/pdb5CUY/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.252 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.189 (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: 190.48 kDa 
• Atom Count: 13,374 
• Modeled Residue Count: 1,568 
• Deposited Residue Count: 1,656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acidocalcisomal pyrophosphatase	A, B, C, D	414	Trypanosoma brucei brucei TREU927	Mutation(s): 1  Gene Names: Tb11.02.4930 EC: 3.6.1.1
UniProt
Find proteins for Q384W3 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q384W3  Go to UniProtKB:  Q384W3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	E [auth A], G [auth B], I [auth C], K [auth D]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
MG	F [auth A], H [auth B], J [auth C], L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.252 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.189 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 199.917	α = 90
b = 70.137	β = 106.38
c = 141.759	γ = 90

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): Yang, Y.Y., Ko, T.P., 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: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description