7YHJ

Effector binding domain of LysR-Type transcription factor LrhA from E. coli

• PDB DOI: https://doi.org/10.2210/pdb7YHJ/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-07-13 Released: 2022-08-10 
• Deposition Author(s): Xie, C., Jiang, X.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 0.338 
• R-Value Work: 0.321 
• R-Value Observed: 0.322 

Literature

Effector binding domain of LysR-Type transcription factor LrhA from E. coli

Xie, C., Jiang, X.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 284.99 kDa 
• Atom Count: 11,848 
• Modelled Residue Count: 1,532 
• Deposited Residue Count: 2,552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable HTH-type transcriptional regulator LrhA	A, B, C, D, E, F, G, H	319	Escherichia coli	Mutation(s): 0  Gene Names: lrhA, genR, b2289, JW2284
UniProt
Find proteins for P36771 (Escherichia coli (strain K12)) Explore P36771  Go to UniProtKB:  P36771

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	J [auth G]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	I [auth D], K [auth G]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.24 Å
• R-Value Free: 0.338 
• R-Value Work: 0.321 
• R-Value Observed: 0.322 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.682	α = 90
b = 169.312	β = 90
c = 190.852	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
Coot	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-08-10 
Deposition Author(s): Xie, C., Jiang, X.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• Version 1.0: 2022-08-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description