6XYN | pdb_00006xyn

Crystal structure of a proteolytic fragment of NarQ comprising sensor and TM domains

• PDB DOI: https://doi.org/10.2210/pdb6XYN/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-01-30 Released: 2020-03-04 
• Deposition Author(s): Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Gordeliy, V.
• Funding Organization(s): Russian Science Foundation, French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a proteolytic fragment of the sensor histidine kinase NarQ

Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Gordeliy, V.

(2020) Crystals (Basel) 

• DOI: https://doi.org/10.3390/cryst10030149

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: 26.87 kDa 
• Atom Count: 1,331 
• Modeled Residue Count: 158 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrate/nitrite sensor histidine kinase NarQ	A	236	Escherichia coli	Mutation(s): 0  Gene Names: narQ, b2469, JW2453 EC: 2.7.13.3 Membrane Entity: Yes
UniProt
Find proteins for P27896 (Escherichia coli (strain K12)) Explore P27896  Go to UniProtKB:  P27896

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3 (Subject of Investigation/LOI)	B [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.283	α = 90
b = 51.283	β = 90
c = 182.988	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Gushchin, I., Melnikov, I., Polovinkin, V., Ishchenko, A., Gordeliy, V.

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Funding Organization	Location	Grant Number
Russian Science Foundation	Russian Federation	18-74-10053
French National Research Agency	France	ANR-10-INSB-05-02
French National Research Agency	France	ANR-10-LABX-49-01

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description