6NSM

TetR family transcriptional regulator CifR C99T-C107S-C181R Cysteines mutant complexed with 26bp double-strand operator DNA

• PDB DOI: https://doi.org/10.2210/pdb6NSM/pdb
• NAKB: 6NSM

• Classification: TRANSCRIPTION/DNA
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14, 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 

Starting Model: experimental

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

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)

Biological Assembly Evidence: gel filtration, native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 59.92 kDa 
• Atom Count: 4,108 
• Modelled Residue Count: 437 
• Deposited Residue Count: 448 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TetR family transcriptional regulator CifR	A, B	198	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 3  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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	C	26	Pseudomonas aeruginosa

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (26-MER)	D	26	Pseudomonas aeruginosa

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.248 
• R-Value Work: 0.228 
• R-Value Observed: 0.229 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.15785/SBGRID/1075

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.329	α = 90
b = 167.897	β = 90
c = 82.538	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-29 
Deposition Author(s): He, S., Simard, A.R., Madden, D.R.

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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  

• 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, Other, Refinement description, Source and taxonomy, Structure summary