4LSM | pdb_00004lsm

Crystal structure of a glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi

• PDB DOI: https://doi.org/10.2210/pdb4LSM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Trypanosoma cruzi strain CL Brener
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-22 Released: 2013-08-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a glycosomal glyceraldehyde-3-phosphate dehydrogenase from Trypanosoma cruzi

Edwards, T.E., Abendroth, J.

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 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 76.78 kDa 
• Atom Count: 5,798 
• Modeled Residue Count: 662 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyceraldehyde 3-phosphate dehydrogenase, cytosolic	A, B	346	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053510105.230 EC: 1.2.1.12
UniProt
Find proteins for Q4DZT1 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DZT1  Go to UniProtKB:  Q4DZT1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], H [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO	D [auth A], E [auth A], F [auth A], G [auth A], I [auth B], J [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34LSM

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.49	α = 90
b = 80.49	β = 90
c = 203.06	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description