3BWC | pdb_00003bwc

Crystal structure of spermidine synthase from Trypanosoma cruzi in complex with SAM at 2.3 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3BWC/pdb

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


• Deposited: 2008-01-09 Released: 2008-04-01 
• Deposition Author(s): Bosch, J., Arakaki, T.L., Le Trong, I., Merritt, E.A., Hol, W.G.J., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of spermidine synthase from Trypanosoma cruzi.

Bosch, J., Arakaki, T.L., Le Trong, I., Merritt, E.A., 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: 70 kDa 
• Atom Count: 4,921 
• Modeled Residue Count: 553 
• 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

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A], E [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
BME	D [auth A], F [auth B]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

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: 2.30 Å
• R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.08	α = 90
b = 99.943	β = 106.26
c = 69.991	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-01 
Deposition Author(s): Bosch, J., Arakaki, T.L., Le Trong, I., Merritt, E.A., 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: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection