2ZKZ

Crystal structure of the transcriptional repressor PagR of Bacillus anthracis

PDB DOI: https://doi.org/10.2210/pdb2ZKZ/pdb

Classification: TRANSCRIPTION
Organism(s): Bacillus anthracis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-04-01 Released: 2009-04-07
Deposition Author(s): Zhao, H., Volkov, A., Veldore, V.H., Varughese, K.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.266
R-Value Work: 0.246

wwPDB Validation 3D Report Full Report

This is version 1.3 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

PubMed: 19926656 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1099/mic.0.033548-0
Primary Citation of 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
Modelled Residue Count: 341
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional repressor pagR	A, B, C, D	99	Bacillus anthracis	Mutation(s): 0 Gene Names: pagR, tcrA
UniProt
Find proteins for O31178 (Bacillus anthracis) Explore O31178 Go to UniProtKB: O31178
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O31178
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.266
R-Value Work: 0.246
Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.01	α = 90
b = 73.01	β = 90
c = 151.12	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Varughese, K.I.

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.