Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.30 kDa 
• Atom Count: 3029 
• Modelled Residue Count: 359 
• Deposited Residue Count: 375 
• Unique protein chains: 1

1ZES

BeF3- activated PhoB receiver domain

• PDB DOI: 10.2210/pdb1ZES/pdb

• Classification: TRANSCRIPTION ACTIVATOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2005-04-19 Released: 2005-09-20 
• Deposition Author(s): Bachhawat, P., Montelione, G.T., Stock, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.240 
• R-Value Work: 0.189 
• R-Value Observed: 0.194 

Literature

Mechanism of Activation for Transcription Factor PhoB Suggested by Different Modes of Dimerization in the Inactive and Active States.

Bachhawat, P., Swapna, G.V., Montelione, G.T., Stock, A.M.

(2005) Structure 13: 1353-1363

• PubMed: 16154092 
• DOI: 10.1016/j.str.2005.06.006
• Primary Citation of Related Structures:  
  1ZES


• PubMed Abstract: 
  

Response regulators (RRs), which undergo phosphorylation/dephosphorylation at aspartate residues, are highly prevalent in bacterial signal transduction. RRs typically contain an N-terminal receiver domain that regulates the activities of a C-terminal DNA binding domain in a phosphorylation-dependent manner. We present crystallography and solution NMR data for the receiver domain of Escherichia coli PhoB which show distinct 2-fold symmetric dimers in the inactive and active states. These structures, together with the previously determined structure of the C-terminal domain of PhoB bound to DNA, define the conformation of the active transcription factor and provide a model for the mechanism of activation in the OmpR/PhoB subfamily, the largest group of RRs. In the active state, the receiver domains dimerize with 2-fold rotational symmetry using their alpha4-beta5-alpha5 faces, while the effector domains bind to DNA direct repeats with tandem symmetry, implying a loss of intramolecular interactions.

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Organizational Affiliation: 

Center for Advanced Biotechnology and Medicine, Piscataway, NJ 08854, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphate regulon transcriptional regulatory protein phoB	A, B, C	125	Escherichia coli	Mutation(s): 1  Gene Names: phoB
UniProt
Find proteins for P0AFJ5 (Escherichia coli (strain K12)) Explore P0AFJ5  Go to UniProtKB:  P0AFJ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEF	E [auth A], G [auth B], I [auth C]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	D [auth A], F [auth B], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.240 
• R-Value Work: 0.189 
• R-Value Observed: 0.194 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.869	α = 90
b = 77.869	β = 90
c = 109.071	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-19 
• Released Date: 2005-09-20 
Deposition Author(s): Bachhawat, P., Montelione, G.T., Stock, A.M.

Revision History  

• Version 1.0: 2005-09-20
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations