6M8O

Crystal structure of the receiver domain of LytR from Staphylococcus aureus

• PDB DOI: https://doi.org/10.2210/pdb6M8O/pdb

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


• Deposited: 2018-08-22 Released: 2018-09-19 
• Deposition Author(s): Shala-Lawrence, A., Audette, G.F.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Crystal structure of the receiver domain of LytR from Staphylococcus aureus

Shala-Lawrence, A., Audette, G.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 15.14 kDa 
• Atom Count: 948 
• Modelled Residue Count: 118 
• Deposited Residue Count: 134 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	A	134	Staphylococcus aureus	Mutation(s): 0  Gene Names: C3B39_09020, EP54_06415, EQ90_12235, HMPREF3211_02791
UniProt
Find proteins for P60611 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore P60611  Go to UniProtKB:  P60611

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.237 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.747	α = 90
b = 84.747	β = 90
c = 157.304	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASES	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-09-19 
Deposition Author(s): Shala-Lawrence, A., Audette, G.F.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	RGPIN-06218-2014

Revision History  

• Version 1.0: 2018-09-19
  Type: Initial release
  
• Version 1.1: 2020-01-08
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description