4P8R | pdb_00004p8r

Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma brucei

• PDB DOI: https://doi.org/10.2210/pdb4P8R/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-03-31 Released: 2014-06-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Structure of a glycosomal glyceraldehyde 3-phosphate dehydrogenase from Trypanosoma brucei

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Lorimer, D., Edwards, T.E.

To be published.

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: 149.47 kDa 
• Atom Count: 10,763 
• Modeled Residue Count: 1,323 
• Deposited Residue Count: 1,356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-phosphate dehydrogenase, cytosolic	A, B, C, D	339	Trypanosoma brucei brucei TREU927	Mutation(s): 0  Gene Names: Tb10.6k15.3850 EC: 1.2.1.12
UniProt
Find proteins for Q38AR9 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38AR9  Go to UniProtKB:  Q38AR9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], G [auth B], I [auth C], J [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
MG	F [auth A], H [auth B], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34P8R

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.7	α = 90
b = 86.7	β = 90
c = 701.37	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
ARP	model building
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2015-09-30
  Changes: Data collection
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Derived calculations