6WON

Crystal structure of acetoin dehydrogenase YohF from Salmonella typhimurium

• PDB DOI: https://doi.org/10.2210/pdb6WON/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-25 Released: 2020-05-13 
• Deposition Author(s): Stogios, P.J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.207 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 

Starting Model: experimental

Literature

Crystal structure of acetoin dehydrogenase YohF from Salmonella typhimurium

Stogios, P.J.

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)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 216.57 kDa 
• Atom Count: 15,700 
• Modelled Residue Count: 1,946 
• Deposited Residue Count: 2,040 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YohF	A, B, C, D, E, F, G, H	255	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: yohF, STM2171 EC: 1
UniProt
Find proteins for Q8ZNM5 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZNM5  Go to UniProtKB:  Q8ZNM5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	K [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 0.207 
• R-Value Work: 0.160 
• R-Value Observed: 0.161 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.549	α = 90
b = 114.171	β = 90
c = 219.342	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-05-13 
Deposition Author(s): Stogios, P.J., Skarina, T., Mesa, N., Endres, M., Savchenko, A., Joachimiak, A., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description