3HTI | pdb_00003hti

Crystal structure of multidrug binding protein EbrR complexed with malachite green

• PDB DOI: https://doi.org/10.2210/pdb3HTI/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: 2.50 Å
• R-Value Free: 
  0.286 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

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)

Macromolecule Content 

• Total Structure Weight: 23.6 kDa 
• Atom Count: 1,356 
• Modeled Residue Count: 173 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EbrA repressor	A	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MGR	B [auth A]	MALACHITE GREEN C23 H25 N2 VFCNQNZNPKRXIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.286 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.254 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.91	α = 90
b = 59.91	β = 90
c = 110.236	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
CNS	refinement
d*TREK	data reduction
d*TREK	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