Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.45 kDa 
• Atom Count: 1835 
• Modelled Residue Count: 213 
• Deposited Residue Count: 213 
• Unique protein chains: 1

1B4B

STRUCTURE OF THE OLIGOMERIZATION DOMAIN OF THE ARGININE REPRESSOR FROM BACILLUS STEAROTHERMOPHILUS

• PDB DOI: 10.2210/pdb1B4B/pdb

• Classification: REPRESSOR
• Organism(s): Geobacillus stearothermophilus
• Mutation(s): No 


• Deposited: 1998-12-18 Released: 1999-06-15 
• Deposition Author(s): Ni, J., Sakanyan, V., Charlier, D., Glansdorff, N., Van Duyne, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Literature

Structure of the arginine repressor from Bacillus stearothermophilus.

Ni, J., Sakanyan, V., Charlier, D., Glansdorff, N., Van Duyne, G.D.

(1999) Nat Struct Biol 6: 427-432

• PubMed: 10331868 
• DOI: 10.1038/8229
• Primary Citation of Related Structures:  
  1B4A, 1B4B


• PubMed Abstract: 
  

The arginine repressor (ArgR) is a hexameric DNA-binding protein that plays a multifunctional role in the bacterial cell. Here, we present the 2.5 A structure of apo-ArgR from Bacillus stearothermophilus and the 2.2 A structure of the hexameric ArgR oligomerization domain with bound arginine. This first view of intact ArgR reveals an approximately 32-symmetric hexamer of identical subunits, with six DNA-binding domains surrounding a central oligomeric core. The difference in quaternary organization of subunits in the arginine-bound and apo forms provides a possible explanation for poor operator binding by apo-ArgR and for high affinity binding in the presence of arginine.

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Related Citations: 

• The Crystal Structure of Arginine Repressor
  Ni, J.
  (1998) Thesis --: --

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Organizational Affiliation: 

Department of Biochemistry & Biophysics and Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia 19104, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ARGININE REPRESSOR	A, B, C	71	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: argR
UniProt
Find proteins for O31408 (Geobacillus stearothermophilus) Explore O31408  Go to UniProtKB:  O31408

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	D [auth A], E [auth B], F [auth B]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82	α = 90
b = 82	β = 90
c = 67.2	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-12-18 
• Released Date: 1999-06-15 
Deposition Author(s): Ni, J., Sakanyan, V., Charlier, D., Glansdorff, N., Van Duyne, G.D.

Revision History  

• Version 1.0: 1999-06-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model