2OZ6

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

Experimental Data Snapshot

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

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


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

  • 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virulence Factor Regulator207Pseudomonas aeruginosaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55222
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CMP
Query on CMP
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
Binding Affinity Annotations 
IDSourceBinding 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 = 69.95α = 90
b = 69.95β = 90
c = 147.49γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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