2PWP | pdb_00002pwp

Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermidine

• PDB DOI: https://doi.org/10.2210/pdb2PWP/pdb

• Classification: TRANSFERASE
• Organism(s): Plasmodium falciparum 3D7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-11 Released: 2007-05-22 
• Deposition Author(s): Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.232 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.192 (DCC) 

Starting Model: experimental

Literature

Crystal structure of spermidine synthase from Plasmodium falciparum in complex with spermidine.

Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R.

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.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.3 kDa 
• Atom Count: 7,110 
• Modeled Residue Count: 835 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B, C	282	Plasmodium falciparum 3D7	Mutation(s): 0  Gene Names: PF11_0301 EC: 2.5.1.16
UniProt
Find proteins for Q8II73 (Plasmodium falciparum (isolate 3D7)) Explore Q8II73  Go to UniProtKB:  Q8II73

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPD	D [auth A], F [auth B], I [auth C]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
SO4	G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], H [auth B], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.232 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.192 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 198.969	α = 90
b = 134.498	β = 95.88
c = 48.711	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-22 
Deposition Author(s): Qiu, W., Dong, A., Ren, H., Wu, H., Zhao, Y., Schapira, M., Wasney, G., Vedadi, M., Lew, J., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Sundstrom, M., Plotnikov, A.N., Bochkarev, A., Hui, R., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2007-05-22
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description