8A52 | pdb_00008a52

Crystal structure of a chimeric LOV-Histidine kinase SB2F1 (asymmetrical variant, trigonal form with long c-axis)

• PDB DOI: https://doi.org/10.2210/pdb8A52/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas putida KT2440, Bradyrhizobium diazoefficiens USDA 110
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-14 Released: 2023-12-27 
• Deposition Author(s): Batra-Safferling, R., Arinkin, V., Granzin, J.
• Funding Organization(s): German Federal Ministry for Education and Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 
  0.295 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Literature

Dimer asymmetry in signaling of blue-light sensor histidine kinases

Arinkin, V., Stadler, A.M., Meier, S.S.M., Jaeger, K.E., Moglich, A., Krauss, U., Batra-Safferling, R.

(2025) bioRxiv 

• DOI: https://doi.org/10.1101/2025.10.24.684451

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: 88.66 kDa 
• Atom Count: 5,784 
• Modeled Residue Count: 728 
• Deposited Residue Count: 776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative Sensory box protein,Putative Sensory box protein,Sensor protein FixL	A, B	388	Pseudomonas putida KT2440, Bradyrhizobium diazoefficiens USDA 110 This entity is chimeric	Mutation(s): 0  Gene Names: PP_2739 EC: 2.7.13.3
UniProt
Find proteins for P23222 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore P23222  Go to UniProtKB:  P23222
Find proteins for Q88JB0 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JB0  Go to UniProtKB:  Q88JB0
UniProt Groups	P23222Q88JB0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	C [auth A], E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
FMN (Subject of Investigation/LOI)	D [auth A], F [auth B]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free:  0.295 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.246	α = 90
b = 138.246	β = 90
c = 94.99	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
SHELXD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Batra-Safferling, R., Arinkin, V., Granzin, J.

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Funding Organization	Location	Grant Number
German Federal Ministry for Education and Research	Germany	FKZ 031A16

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary
• Version 1.2: 2026-04-01
  Changes: Database references, Refinement description