3BWB

Crystal structure of the apo form of spermidine synthase from Trypanosoma cruzi at 2.5 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BWB/pdb

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


• Deposited: 2008-01-08 Released: 2008-04-01 
• Deposition Author(s): Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 

Literature

Crystal structure of spermidine synthase from Trypanosoma cruzi.

Bosch, J., Hol, W.G.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)

Macromolecule Content

• Total Structure Weight: 69.05 kDa 
• Atom Count: 4,671 
• Modelled Residue Count: 571 
• Deposited Residue Count: 608 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B	304	Trypanosoma cruzi strain CL Brener	Mutation(s): 0  Gene Names: Tc00.1047053510339.50 EC: 2.5.1.16
UniProt
Find proteins for Q4DA73 (Trypanosoma cruzi (strain CL Brener)) Explore Q4DA73  Go to UniProtKB:  Q4DA73

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.248 
• R-Value Work: 0.198 
• R-Value Observed: 0.201 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.669	α = 90
b = 96.996	β = 106.33
c = 69.649	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
XDS	data reduction
XSCALE	data scaling
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Bosch, J., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2008-04-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary