6UXT

Crystal structure of unknown function protein yfdX from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb6UXT/pdb

• Classification: STRUCTURAL GENOMICS
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-11-08 Released: 2019-11-20 
• Deposition Author(s): Chang, C., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 

Literature

Crystal structure of unknown function protein yfdX from Shigella flexneri

Chang, C., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 163.03 kDa 
• Atom Count: 11,062 
• Modelled Residue Count: 1,306 
• Deposited Residue Count: 1,488 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfdX protein	A, B, C, D, E, F, G, H	186	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: yfdX,

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	L [auth F]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
PGE	I [auth B], K [auth E]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	J [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.200 
• R-Value Work: 0.170 
• R-Value Observed: 0.172 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m36uxt

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.579	α = 97.35
b = 92.92	β = 98.44
c = 93.469	γ = 95.46

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Currently 6UXT does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Chang, C., Skarina, T., Savchenko, A., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description