Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 64.64 kDa 
• Atom Count: 4564 
• Modelled Residue Count: 578 
• Deposited Residue Count: 588 
• Unique protein chains: 1

1IXC

Crystal structure of CbnR, a LysR family transcriptional regulator

• PDB DOI: 10.2210/pdb1IXC/pdb

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


• Deposited: 2002-06-18 Released: 2003-06-18 
• Deposition Author(s): Muraoka, S., Okumura, R., Ogawa, N., Miyashita, K., Senda, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 

Literature

Crystal Structure of a Full-length LysR-type Transcriptional Regulator, CbnR: Unusual Combination of Two Subunit Forms and Molecular Bases for Causing and Changing DNA Bend

Muraoka, S., Okumura, R., Ogawa, N., Nonaka, T., Miyashita, K., Senda, T.

(2003) J Mol Biol 328: 555-566

• PubMed: 12706716 
• DOI: 10.1016/s0022-2836(03)00312-7
• Primary Citation of Related Structures:  
  1IXC, 1IZ1


• PubMed Abstract: 
  

The LysR-type transcriptional regulator (LTTR) proteins are one of the most common transcriptional regulators in prokaryotes. Here we report the crystal structure of CbnR, which is one of the LTTRs derived from Ralstonia eutropha NH9. This is the first crystal structure of a full-length LTTR. CbnR was found to form a homo-tetramer, which seems to be a biologically active form. Surprisingly, the tetramer can be regarded as a dimer of dimers, whereby each dimer is composed of two subunits in different conformations. In the CbnR tetramer, the DNA-binding domains are located at the V-shaped bottom of the main body of the tetramer, and seem to be suitable to interact with a long stretch of the promoter DNA, which is approximately 60bp. Interaction between the four DNA-binding domains and the two binding sites on the target DNA is likely to bend the target DNA along the V-shaped bottom of the CbnR tetramer. The relaxation of the bent DNA, which occurs upon inducer binding to CbnR, seems to be associated with a quaternary structure change of the tetramer.

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Organizational Affiliation: 

Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LysR-type regulatory protein	A, B	294	Cupriavidus necator	Mutation(s): 5  Gene Names: cbnR, BJN34_37375
UniProt
Find proteins for Q9WXC7 (Cupriavidus necator) Explore Q9WXC7  Go to UniProtKB:  Q9WXC7

Small Molecules

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: 2.20 Å
• R-Value Free: 0.245 
• R-Value Work: 0.218 
• R-Value Observed: 0.219 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.22	α = 90
b = 100.856	β = 90
c = 87.735	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-06-18 
• Released Date: 2003-06-18 
Deposition Author(s): Muraoka, S., Okumura, R., Ogawa, N., Miyashita, K., Senda, T.

Revision History  

• Version 1.0: 2003-06-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance