4XJY | pdb_00004xjy

Periplasmic repressor protein YfiR

• PDB DOI: https://doi.org/10.2210/pdb4XJY/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-09 Released: 2016-01-20 
• Deposition Author(s): Kauer, S., Schirmer, T.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Periplasmic repressor protein YfiR at 1.8 Angstroms resolution

Kauer, S., Schirmer, T.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 74.23 kDa 
• Atom Count: 5,012 
• Modeled Residue Count: 595 
• Deposited Residue Count: 656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfiR	A, B, C, D	164	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: yfiR, PA1121
UniProt
Find proteins for Q9I4L4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I4L4  Go to UniProtKB:  Q9I4L4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P33	E [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
TLA	F [auth B], G [auth C], H [auth D]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.691	α = 90
b = 68.073	β = 111.42
c = 71.989	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
SHELX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Kauer, S., Schirmer, T.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A-138414

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 2.0: 2017-09-13
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations
• Version 2.1: 2024-11-06
  Changes: Advisory, Data collection, Database references, Structure summary