7TRW

Crystal Structure of the C-terminal Ligand-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis

• PDB DOI: https://doi.org/10.2210/pdb7TRW/pdb

• Classification: TRANSCRIPTION
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-31 Released: 2022-02-09 
• Deposition Author(s): Kim, Y., Tesar, C., Crawford, M., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Crystal Structure of the C-terminal Ligand-Binding Domain of the LysR family Transcriptional Regulator YfbA from Yersinia pestis

Kim, Y., Tesar, C., Crawford, M., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Macromolecule Content

• Total Structure Weight: 24.25 kDa 
• Atom Count: 1,764 
• Modelled Residue Count: 213 
• Deposited Residue Count: 217 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR-family transcriptional regulatory protein	A	217	Yersinia pestis CO92	Mutation(s): 0  Gene Names: lysR10, y2171, YP_1951
UniProt
Find proteins for A0A380PDL3 (Yersinia pestis) Explore A0A380PDL3  Go to UniProtKB:  A0A380PDL3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3HB (Subject of Investigation/LOI)	B [auth A]	3-HYDROXYBENZOIC ACID C7 H6 O3 IJFXRHURBJZNAO-UHFFFAOYSA-N
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.28 Å
• R-Value Free: 0.234 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.073	α = 90
b = 86.073	β = 90
c = 69.28	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MLPHARE	phasing
SHELXD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-02-09 
Deposition Author(s): Kim, Y., Tesar, C., Crawford, M., Endres, M., Babnigg, G., Schneewind, O., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-02-09
  Type: Initial release