6DK4 | pdb_00006dk4

Crystal structure of Campylobacter jejuni peroxide stress regulator

PDB DOI: https://doi.org/10.2210/pdb6DK4/pdb

Classification: METAL TRANSPORT
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-05-28 Released: 2018-06-13
Deposition Author(s): Sarvan, S., Brunzelle, J.S., Couture, J.F.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.270 (Depositor), 0.275 (DCC)
R-Value Work:
0.215 (Depositor), 0.223 (DCC)
R-Value Observed:
0.218 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of Campylobacter jejuni peroxide regulator.

Sarvan, S., Charih, F., Butcher, J., Brunzelle, J.S., Stintzi, A., Couture, J.F.

(2018) FEBS Lett 592: 2351-2360

PubMed: 29856899 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13120
Primary Citation Related Structures:
6DK4

PubMed Abstract:
In Campylobacter jejuni (Cj), the metal-cofactored peroxide response regulator (PerR) transcription factor allows C. jejuni to respond to oxidative stresses. The crystal structure of the metalated form of CjPerR shows that the protein folds as an asymmetric dimer displaying structural differences in the orientation of its DNA-binding domain. Comparative analysis shows that such asymmetry is a conserved feature among crystallized PerR proteins, and mutational analysis reveals that residues found in the first α-helix of CjPerR contribute to DNA binding. These studies present the structure of CjPerR protein and highlight structural heterogeneity in the orientation of the metalated PerR DNA-binding domain which may underlie the ability of PerR to recognize DNA, control gene expression, and contribute to bacterial pathogenesis.

Organizational Affiliation

Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, University of Ottawa, Canada.

Macromolecule Content

Total Structure Weight: 34.21 kDa
Atom Count: 2,082
Modeled Residue Count: 248
Deposited Residue Count: 284
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric uptake regulation protein	A, B	142	Campylobacter jejuni	Mutation(s): 0 Gene Names: perR, fur, Cj0322
UniProt
Find proteins for Q0PBI7 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0PBI7 Go to UniProtKB: Q0PBI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0PBI7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], G [auth A], H [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.270 (Depositor), 0.275 (DCC)
R-Value Work: 0.215 (Depositor), 0.223 (DCC)
R-Value Observed: 0.218 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.11	α = 90
b = 70.186	β = 90
c = 85.158	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
autoPROC	data scaling
AutoSol	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-06-13

Deposition Author(s):

Sarvan, S.

Brunzelle, J.S.

Couture, J.F.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2018-06-13
Type: Initial release
Version 1.1: 2018-09-12
Changes: Data collection, Database references
Version 1.2: 2020-01-08
Changes: Author supporting evidence
Version 1.3: 2024-03-06
Changes: Data collection, Database references, Refinement description