4YN8 | pdb_00004yn8

Crystal Structure of Response Regulator ChrA in Heme-Sensing Two Component System

• PDB DOI: https://doi.org/10.2210/pdb4YN8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-03-09 Released: 2015-08-19 
• Deposition Author(s): Doi, A., Nakamura, H., Shiro, Y., Sugimoto, H.
• Funding Organization(s): KAKENHI

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.202 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Structure of the response regulator ChrA in the haem-sensing two-component system of Corynebacterium diphtheriae.

Doi, A., Nakamura, H., Shiro, Y., Sugimoto, H.

(2015) Acta Crystallogr F Struct Biol Commun 71: 966-971

• PubMed: 26249683 
• DOI: https://doi.org/10.1107/S2053230X15009838
• Primary Citation Related Structures: 
  4YN8


• PubMed Abstract: 
  

  ChrA is a response regulator (RR) in the two-component system involved in regulating the degradation and transport of haem (Fe-porphyrin) in the pathogen Corynebacterium diphtheriae. Here, the crystal structure of full-length ChrA is described at a resolution of 1.8 Å. ChrA consists of an N-terminal regulatory domain, a long linker region and a C-terminal DNA-binding domain. A structural comparison of ChrA with other RRs revealed substantial differences in the relative orientation of the two domains and the conformation of the linker region. The structural flexibility of the linker could be an important feature in rearrangement of the domain orientation to create a dimerization interface to bind DNA during haem-sensing signal transduction.

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Organizational Affiliation: 
• RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.19 kDa 
• Atom Count: 1,800 
• Modeled Residue Count: 201 
• Deposited Residue Count: 203 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator ChrA	A	203	Corynebacterium diphtheriae	Mutation(s): 1  Gene Names: chrA
UniProt
Find proteins for Q9RPE9 (Corynebacterium diphtheriae) Explore Q9RPE9  Go to UniProtKB:  Q9RPE9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.202 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.88	α = 90
b = 84.88	β = 90
c = 169.3	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
BALBES	phasing
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-08-19 
Deposition Author(s): Doi, A., Nakamura, H., Shiro, Y., Sugimoto, H.

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Funding Organization	Location	Grant Number
KAKENHI	Japan	24687015
KAKENHI	Japan	25121739
KAKENHI	Japan	23121531

Revision History  

• Version 1.0: 2015-08-19
  Type: Initial release
  
• Version 1.1: 2020-02-05
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description