6NSN

TetR family transcriptional regulator CifR C99T-C181R Cysteines mutant complexed with 26bp double-strand operator DNA

PDB DOI: https://doi.org/10.2210/pdb6NSN/pdb
NAKB: 6NSN

Classification: TRANSCRIPTION/DNA
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-01-25 Released: 2020-01-29
Deposition Author(s): He, S., Simard, A.R., Madden, D.R.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), Cystic Fibrosis Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.242
R-Value Work: 0.223
R-Value Observed: 0.224

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Molecular basis for the transcriptional regulation of an epoxide-based virulence circuit in Pseudomonas aeruginosa

He, S., Taher, N.M., Simard, A.R., Hvorecny, K.L., Ragusa, M.J., Bahl, C.D., Hickman, A.B., Dyda, F., Madden, D.R.

(2024) bioRxiv

DOI: https://doi.org/10.1101/2024.01.16.572601

Macromolecule Content

Total Structure Weight: 60.09 kDa
Atom Count: 4,144
Modelled Residue Count: 438
Deposited Residue Count: 448
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator CifR	A	198	Pseudomonas aeruginosa	Mutation(s): 2 Gene Names: PA14_26140
UniProt
Find proteins for Q9HZR6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZR6 Go to UniProtKB: Q9HZR6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HZR6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator CifR	B	198	Pseudomonas aeruginosa	Mutation(s): 2 Gene Names: PA14_26140
UniProt
Find proteins for Q9HZR6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HZR6 Go to UniProtKB: Q9HZR6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HZR6
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	C	26	Pseudomonas aeruginosa
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	D	26	Pseudomonas aeruginosa
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
CSD Query on CSD	B	L-PEPTIDE LINKING	C₃ H₇ N O₄ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.242
R-Value Work: 0.223
R-Value Observed: 0.224
Space Group: P 2₁ 2₁ 2
Diffraction Data: https://doi.org/10.15785/SBGRID/1074

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.968	α = 90
b = 166.685	β = 90
c = 82.979	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

He, S.

Simard, A.R.

Madden, D.R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01-AI091699
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20-GM113132
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	P30-DK117469
Cystic Fibrosis Foundation	United States	STANTO19R0

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-01-31
Changes: Database references, Source and taxonomy, Structure summary
Version 1.3: 2024-02-14
Changes: Source and taxonomy, Structure summary
Version 2.0: 2024-07-17
Type: Coordinate replacement
Reason: Real space R-factor
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary