5E20 | pdb_00005e20

Crystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the 2,3-dichlorophenol bound form

• PDB DOI: https://doi.org/10.2210/pdb5E20/pdb

• Classification: TRANSCRIPTION
• Organism(s): Dehalococcoides mccartyi CBDB1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-30 Released: 2016-10-05 
• Deposition Author(s): Quezada, C.P., Dunstan, M.S., Fisher, K., Leys, D.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of RdhRCbdbA1625 provide insight into sensing of chloroaromatic compounds by MarR-type regulators

Quezada, C.P., Dunstan, M.S., Fisher, K., Leys, D.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.18 kDa 
• Atom Count: 1,543 
• Modeled Residue Count: 169 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MarR family	A	180	Dehalococcoides mccartyi CBDB1	Mutation(s): 0  Gene Names: rdhR, btf_1489
UniProt
Find proteins for A0A1I9GEQ5 (Dehalococcoides mccartyi (strain CBDB1)) Explore A0A1I9GEQ5  Go to UniProtKB:  A0A1I9GEQ5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5JF	B [auth A]	2,3-dichlorophenol C6 H4 Cl2 O UMPSXRYVXUPCOS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.32	α = 90
b = 71.32	β = 90
c = 87.12	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Quezada, C.P., Dunstan, M.S., Fisher, K., Leys, D.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	DEHALORES206080

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Author supporting evidence, Data collection, Database references, Refinement description