2ZKZ | pdb_00002zkz

Crystal structure of the transcriptional repressor PagR of Bacillus anthracis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.266 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.246 (Depositor), 0.248 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2ZKZ

This is version 1.4 of the entry. See complete history. 

Literature

Crystal structure of the transcriptional repressor PagR of Bacillus anthracis

Zhao, H., Volkov, A., Veldore, V.H., Hoch, J.A., Varughese, K.I.

(2010) Microbiology (N Y) 156: 385-391

  • DOI: https://doi.org/10.1099/mic.0.033548-0
  • Primary Citation Related Structures: 
    2ZKZ

  • PubMed Abstract: 

    PagR is a transcriptional repressor in Bacillus anthracis that controls the chromosomal S-layer genes eag and sap, and downregulates the protective antigen pagA gene by direct binding to their promoter regions. The PagR protein sequence is similar to those of members of the ArsR repressor family involved in the repression of arsenate-resistance genes in numerous bacteria. The crystal structure of PagR was solved using multi-wavelength anomalous diffraction (MAD) techniques and was refined with 1.8 A resolution diffraction data. The PagR molecules form dimers, as observed in all SmtB/ArsR repressor family proteins. In the crystal lattice four PagR dimers pack together to form an inactive octamer. Model-building studies suggest that the dimer binds to a DNA duplex with a bend of around 4 degrees.

    • Organizational Affiliation: 
    • Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 47.24 kDa 
  • Atom Count: 2,841 
  • Modeled Residue Count: 341 
  • Deposited Residue Count: 396 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional repressor pagR
A, B, C, D
99Bacillus anthracisMutation(s): 0 
Gene Names: pagR, tcrA
UniProt
Find proteins for O31178 (Bacillus anthracis)
Explore O31178 
Go to UniProtKB:  O31178
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO31178
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.246 (Depositor), 0.248 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.01α = 90
b = 73.01β = 90
c = 151.12γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-11-30
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary