6JAF | pdb_00006jaf

Crystal structure of Trypanosoma brucei gambiense glycerol kinase complex with PPi (pyrophosphatase reaction)

• PDB DOI: https://doi.org/10.2210/pdb6JAF/pdb

• Classification: TRANSFERASE
• Organism(s): Trypanosoma brucei gambiense
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-24 Released: 2020-01-29 
• Deposition Author(s): Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., Bringaud, F., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.298 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Glycerol Kinase of African Human Trypanosomes Possesses a Pyrophosphatase Activity.

Balogun, E.O.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 114.49 kDa 
• Atom Count: 7,935 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,036 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycerol kinase	A, B	518	Trypanosoma brucei gambiense	Mutation(s): 0  Gene Names: gk EC: 2.7.1.30
UniProt
Find proteins for D3KVM3 (Trypanosoma brucei gambiense) Explore D3KVM3  Go to UniProtKB:  D3KVM3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POP	C [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
GOL	D [auth A], E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.298 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.055	α = 90
b = 120.461	β = 90
c = 154.558	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): Balogun, E.O., Chishima, T., Ichinose, M., Inaoka, D.K., Kido, Y., Ibrahim, B., Bringaud, F., de Koning, H., McKerrow, J.H., Watanabe, Y., Nozaki, T., Michels, P.A.M., Harada, S., Kita, K., Shiba, T.

Revision History  

• Version 1.0: 2020-01-29
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description