5WIF

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb5WIF/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-07-19 Released: 2017-08-02 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Shatsman, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Yersinia pestis

Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Shatsman, S., Anderson, W.F.

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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 65.05 kDa 
• Atom Count: 4,360 
• Modelled Residue Count: 513 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine N1-acetyltransferase	A, B, C	184	Yersinia pestis	Mutation(s): 0  Gene Names: speG, y1405, YP_2698 EC: 2.3.1.57
UniProt
Find proteins for A0A5P8YIA2 (Yersinia pestis) Explore A0A5P8YIA2  Go to UniProtKB:  A0A5P8YIA2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG5	D [auth B]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C8 H18 O4 YFNKIDBQEZZDLK-UHFFFAOYSA-N
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
BO3	G [auth C]	BORIC ACID B H3 O3 KGBXLFKZBHKPEV-UHFFFAOYSA-N
K	F [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.242 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: I 2 2 2
• Diffraction Data: https://doi.org/10.18430/m35wif

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.596	α = 90
b = 120.114	β = 90
c = 122.752	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-02 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kiryukhina, O., Shatsman, S., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2017-08-02
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description