2ZSU

Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3, P1 form

• PDB DOI: https://doi.org/10.2210/pdb2ZSU/pdb

• Classification: TRANSFERASE
• Organism(s): Pyrococcus horikoshii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2008-10-21 
• Deposition Author(s): Mizutani, H., Kunishima, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 

Starting Model: experimental

Literature

Crystal structure of spermidine synthase from Pyrococcus horikoshii OT3

Mizutani, H., Kunishima, N.

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 192.63 kDa 
• Atom Count: 14,310 
• Modelled Residue Count: 1,654 
• Deposited Residue Count: 1,680 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
spermidine synthase	A, B, C, D, E, F	280	Pyrococcus horikoshii	Mutation(s): 0  EC: 2.5.1.16
UniProt
Find proteins for O57950 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O57950  Go to UniProtKB:  O57950

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AG3	G [auth A], H [auth C], I [auth E]	1-{4-[(3-aminopropyl)amino]butyl}guanidine C8 H21 N5 XYCUJKFFVBCJEF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.207 
• R-Value Observed: 0.207 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.617	α = 99.81
b = 81.842	β = 103.13
c = 96.653	γ = 107.85

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Mizutani, H., Kunishima, N.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description