2OZ6

Crystal Structure of Virulence Factor Regulator from Pseudomonas aeruginosa in complex with cAMP

• PDB DOI: https://doi.org/10.2210/pdb2OZ6/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-24 Released: 2008-03-04 
• Deposition Author(s): Cordes, T.J., Bright, A.R., Forest, K.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.190 

Starting Model: experimental

Literature

Crystal Structure of the Pseudomonas aeruginosa Virulence Factor Regulator.

Cordes, T.J., Worzalla, G.A., Ginster, A.M., Forest, K.T.

(2011) J Bacteriol 193: 4069-4074

• PubMed: 21665969 
• DOI: https://doi.org/10.1128/JB.00666-10
• Primary Citation of Related Structures:  
  2OZ6


• PubMed Abstract: 
  

  Virulence factor regulator (Vfr) enhances Pseudomonas aeruginosa pathogenicity through its role as a global transcriptional regulator. The crystal structure of Vfr shows that it is a winged-helix DNA-binding protein like its homologue cyclic AMP receptor protein (CRP). In addition to an expected primary cyclic AMP-binding site, a second ligand-binding site is nestled between the N-terminal domain and the C-terminal helix-turn-helix domain. Unlike CRP, Vfr is a symmetric dimer in the absence of DNA. Removal of seven disordered N-terminal residues of Vfr prevents the growth of P. aeruginosa.

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Organizational Affiliation: 

University of Wisconsin-Madison, Department of Bacteriology, 1550 Linden Dr., Madison, WI 53706, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 24.2 kDa 
• Atom Count: 1,653 
• Modelled Residue Count: 201 
• Deposited Residue Count: 207 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virulence Factor Regulator	A	207	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: vfr
UniProt
Find proteins for P55222 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P55222  Go to UniProtKB:  P55222

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	B [auth A], C [auth A]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CMP	PDBBind:  2OZ6	Kd: 5500 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.251 
• R-Value Work: 0.190 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.95	α = 90
b = 69.95	β = 90
c = 147.49	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Cordes, T.J., Bright, A.R., Forest, K.T.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2011-08-10
  Changes: Database references
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description