8FV1 | pdb_00008fv1

SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine

• PDB DOI: https://doi.org/10.2210/pdb8FV1/pdb
• Entry: 8FV1 supersedes: 7KY4

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-18 Released: 2023-02-08 
• Deposition Author(s): Tsimbalyuk, S., Forwood, J.K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine, crystal form II

Tsimbalyuk, S., Forwood, J.K.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 81.12 kDa 
• Atom Count: 5,628 
• Modeled Residue Count: 663 
• Deposited Residue Count: 672 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diamine N-acetyltransferase	A [auth C], B [auth A], C [auth B], D	168	Staphylococcus aureus	Mutation(s): 0  Gene Names: res
UniProt
Find proteins for U5NVV0 (Staphylococcus aureus) Explore U5NVV0  Go to UniProtKB:  U5NVV0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	E [auth C], F [auth C], G [auth B], H [auth D]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 161.683	α = 90
b = 161.683	β = 90
c = 161.683	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-08 
Deposition Author(s): Tsimbalyuk, S., Forwood, J.K.
• This entry supersedes: 7KY4

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-02-08
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection