2BJW | pdb_00002bjw

PspF AAA domain

• PDB DOI: https://doi.org/10.2210/pdb2BJW/pdb

• Classification: TRANSCRIPTION
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-02-08 Released: 2005-03-31 
• Deposition Author(s): Rappas, M., Schumacher, J., Beuron, F., Niwa, H., Bordes, P., Wigneshweraraj, S., Keetch, C.A., Robinson, C.V., Buck, M., Zhang, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.208 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structural Insights Into the Activity of Enhancer-Binding Proteins

Rappas, M., Schumacher, J., Beuron, F., Niwa, H., Bordes, P., Wigneshweraraj, S., Keetch, C.A., Robinson, C.V., Buck, M., Zhang, X.

(2005) Science 307: 1972

• PubMed: 15790859 
• DOI: https://doi.org/10.1126/science.1105932
• Primary Citation Related Structures: 
  2BJV, 2BJW


• PubMed Abstract: 
  

  Activators of bacterial sigma54-RNA polymerase holoenzyme are mechanochemical proteins that use adenosine triphosphate (ATP) hydrolysis to activate transcription. We have determined by cryogenic electron microscopy (cryo-EM) a 20 angstrom resolution structure of an activator, phage shock protein F [PspF(1-275)], which is bound to an ATP transition state analog in complex with its basal factor, sigma54. By fitting the crystal structure of PspF(1-275) at 1.75 angstroms into the EM map, we identified two loops involved in binding sigma54. Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54.

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Organizational Affiliation: 
• Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.99 kDa 
• Atom Count: 2,113 
• Modeled Residue Count: 243 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PSP OPERON TRANSCRIPTIONAL ACTIVATOR	A	265	Escherichia coli K-12	Mutation(s): 0
UniProt
Find proteins for P37344 (Escherichia coli (strain K12)) Explore P37344  Go to UniProtKB:  P37344

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.208 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.695	α = 90
b = 113.695	β = 90
c = 39.277	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-31 
Deposition Author(s): Rappas, M., Schumacher, J., Beuron, F., Niwa, H., Bordes, P., Wigneshweraraj, S., Keetch, C.A., Robinson, C.V., Buck, M., Zhang, X.

Revision History  

• Version 1.0: 2005-03-31
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description