1ZES | pdb_00001zes

BeF3- activated PhoB receiver domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1ZES

This is version 1.4 of the entry. See complete history

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

  • DOI: https://doi.org/10.1016/j.str.2005.06.006
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 43.3 kDa 
  • Atom Count: 3,029 
  • Modeled Residue Count: 359 
  • Deposited Residue Count: 375 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphate regulon transcriptional regulatory protein phoB
A, B, C
125Escherichia coliMutation(s): 1 
Gene Names: phoB
UniProt
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
Explore P0AFJ5 
Go to UniProtKB:  P0AFJ5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFJ5
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.869α = 90
b = 77.869β = 90
c = 109.071γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-02-14
    Changes: Data collection, Refinement description