5E1X

Crystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the 3,4-dichlorophenol bound form

PDB DOI: https://doi.org/10.2210/pdb5E1X/pdb

Classification: TRANSCRIPTION
Organism(s): Dehalococcoides mccartyi BTF08
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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.194
R-Value Work: 0.172
R-Value Observed: 0.173

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 21.18 kDa
Atom Count: 1,829
Modelled Residue Count: 168
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator, MarR family	A	180	Dehalococcoides mccartyi BTF08	Mutation(s): 0 Gene Names: rdhR, btf_1489
UniProt
Find proteins for A0A1I9GEQ7 (Dehalococcoides mccartyi BTF08) Explore A0A1I9GEQ7 Go to UniProtKB: A0A1I9GEQ7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1I9GEQ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5JD Query on 5JD Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3,4-dichlorophenol C₆ H₄ Cl₂ O WDNBURPWRNALGP-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.194
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.14	α = 90
b = 71.14	β = 90
c = 87.62	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	DEHALORES206080

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 2.0: 2024-01-10
Changes: Atomic model, Author supporting evidence, Data collection, Database references, Refinement description

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5E1X

Crystal structure of the organohalide sensing RdhR-CbdbA1625 transcriptional regulator in the 3,4-dichlorophenol bound form

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)