5FB2 | pdb_00005fb2

S. aureus MepR F27L Mutant bound to oligodeoxyribonucleotide

• PDB DOI: https://doi.org/10.2210/pdb5FB2/pdb
• NAKB: 5FB2

• Classification: TRANSCRIPTION/DNA
• Organism(s): Staphylococcus aureus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-12-13 Released: 2016-12-14 
• Deposition Author(s): Birukou, I., Newman, C.E., Brennan, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

S. aureus MepR F27L Mutant bound to oligodeoxyribonucleotide

Birukou, I., Newman, C.E., Brennan, R.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.82 kDa 
• Atom Count: 1,382 
• Modeled Residue Count: 143 
• Deposited Residue Count: 145 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MarR family regulatory protein	A	140	Staphylococcus aureus	Mutation(s): 1  Gene Names: mepR
UniProt
Find proteins for Q5Y812 (Staphylococcus aureus) Explore Q5Y812  Go to UniProtKB:  Q5Y812

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*TP*A)-3')	B	5	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.232 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.263	α = 90
b = 97.986	β = 90
c = 106.317	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-14 
Deposition Author(s): Birukou, I., Newman, C.E., Brennan, R.G.

Revision History  

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description