3HTH

Crystal structure of multidrug binding protein EbrR complexed with proflavin

• PDB DOI: https://doi.org/10.2210/pdb3HTH/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Streptomyces lividans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-06-11 Released: 2010-07-14 
• Deposition Author(s): Dong, J., Ni, L., Schumacher, M., Brennan, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Structural plasticity is key to multiple ligand binding by the multidrug binding regulator EbrR

Dong, J., Ni, L., Schumacher, M., Brennan, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

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: 70.39 kDa 
• Atom Count: 4,012 
• Modelled Residue Count: 514 
• Deposited Residue Count: 651 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EbrA repressor	A, B, C	217	Streptomyces lividans	Mutation(s): 0  Gene Names: ebrR
UniProt
Find proteins for Q79SH7 (Streptomyces lividans) Explore Q79SH7  Go to UniProtKB:  Q79SH7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PRL	F [auth A], G [auth B]	PROFLAVIN C13 H11 N3 WDVSHHCDHLJJJR-UHFFFAOYSA-N
NI	D [auth A], E [auth A], H [auth C]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.277 
• R-Value Work: 0.228 
• R-Value Observed: 0.228 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.719	α = 90
b = 99.719	β = 90
c = 133.73	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-14 
Deposition Author(s): Dong, J., Ni, L., Schumacher, M., Brennan, R.

Revision History  

• Version 1.0: 2010-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description