1IY9

Crystal structure of spermidine synthase

• PDB DOI: https://doi.org/10.2210/pdb1IY9/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2002-07-26 Released: 2002-10-30 
• Deposition Author(s): Tan, A.Y., Smith, P.C., Shen, J., Xiao, R., Acton, T., Rost, B., Montelione, G., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Crystal structure of spermidine synthase

Tan, A.Y., Smith, P.C., Shen, J., Xiao, R., Acton, T., Rost, B., Montelione, G., Hunt, J.F.

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: 124.97 kDa 
• Atom Count: 9,099 
• Modelled Residue Count: 1,096 
• Deposited Residue Count: 1,100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A, B, C, D	275	Bacillus subtilis	Mutation(s): 0  EC: 2.5.1.16
UniProt
Find proteins for P70998 (Bacillus subtilis (strain 168)) Explore P70998  Go to UniProtKB:  P70998

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.1	α = 90
b = 105.8	β = 90
c = 121.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-30 
Deposition Author(s): Tan, A.Y., Smith, P.C., Shen, J., Xiao, R., Acton, T., Rost, B., Montelione, G., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2002-10-30
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references