1OJL | pdb_00001ojl

Crystal structure of a sigma54-activator suggests the mechanism for the conformational switch necessary for sigma54 binding

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.308 (Depositor), 0.371 (DCC) 
  • R-Value Work: 
    0.252 (Depositor) 
  • R-Value Observed: 
    0.255 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR.

Sallai, L., Tucker, P.A.

(2005) J Struct Biol 151: 160-170

  • DOI: https://doi.org/10.1016/j.jsb.2005.05.006
  • Primary Citation Related Structures: 
    1OJL

  • PubMed Abstract: 

    The sigma(54)-dependent transcription in bacteria is associated with various stress and growth conditions. Activators of the sigma(54) protein contain a central domain belonging to the AAA+ superfamily of ATPases, members of which function in diverse cellular processes in both prokaryotic and eukaryotic cells. We describe the X-ray structure of an N-terminal domain deletion of the ZraR protein from Salmonella typhimurium, which is a homologue of the general nitrogen regulatory protein NtrC, at 3A resolution. The structure reveals a hexameric ring that is typical for AAA+ containing proteins but which differs from the heptameric ring found in the crystal structure of the AAA+ domain of NtrC1 from Aquifex aeolicus. The dimerisation interface between DNA-binding domains observed in the crystal structure suggests that dodecamers, rather than hexamers, might be the functionally important oligomer.

    • Organizational Affiliation: 
    • European Molecular Biology Laboratory Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 203.41 kDa 
  • Atom Count: 12,594 
  • Modeled Residue Count: 1,624 
  • Deposited Residue Count: 1,824 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
A, B, C, D, E
A, B, C, D, E, F
304Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
UniProt
Find proteins for P25852 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P25852 
Go to UniProtKB:  P25852
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25852
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.308 (Depositor), 0.371 (DCC) 
  • R-Value Work:  0.252 (Depositor) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.44α = 90
b = 114.74β = 90
c = 187.26γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-19
    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: 2018-06-13
    Changes: Data collection, Database references
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Other