2VKF

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified by Flavin-DNA Hybrid Linkers

Grininger, M.Noell, G.Trawoeger, S.Sinner, E.Oesterhelt, D.

(2008) Biointerphases 3: 51

  • DOI: 10.1116/1.2965134
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dodecin from Halobacterium salinarum is a dodecameric, hollow-spherical protein, which unspecifically adopts flavin molecules. Reduction of flavin dodecin holocomplexes induces dissociation into apododecin and free flavin. Unspecific binding and diss ...

    Dodecin from Halobacterium salinarum is a dodecameric, hollow-spherical protein, which unspecifically adopts flavin molecules. Reduction of flavin dodecin holocomplexes induces dissociation into apododecin and free flavin. Unspecific binding and dissociation upon reduction were used as key properties to construct an electrochemically switchable surface, which was able to bind and release dodecin apoprotein depending on the applied potential. A flavin modified electrode surface (electrode-DNA-flavin) was generated by direct adsorption of double stranded DNA (ds-DNA) equipped with flavin and disulfide modifications at opposite ends. While the disulfide functionality enabled anchoring the ds-DNA at the gold surface, the flavin exposed at the surface served as the redox-active dodecin docking site. The structures of protein and flavin-DNA hybrid ligands were optimized and characterized by x-ray structural analysis of the holocomplexes. By surface plasmon resonance (SPR) spectroscopy, the adsorption of flavin modified DNA as well as the binding and the electrochemically induced release of dodecin apoprotein could be shown. When the surface immobilization protocol was changed from direct immobilization of the modified ds-DNA to a protocol, which included the hybridization of flavin and thiol modified DNA at the surface, the resulting monolayer was electrochemically inactive. A possible explanation for the strong influence of the surface immobilization protocol on addressing dodecin by the applied potential is that electron transfer is rather mediated by defects in the monolayer than modified ds-DNA.


    Organizational Affiliation

    Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DODECIN
A
62Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 1 
Find proteins for Q9HPW4 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  Q9HPW4
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CF2
Query on CF2

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A
2'-deoxy-5'-O-{[2-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)ethyl]carbamoyl}guanosine
C25 H26 N10 O7
JIELMHTXDVQHJI-ARFHVFGLSA-N
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.184 
  • Space Group: F 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 141.704α = 90.00
b = 141.704β = 90.00
c = 141.704γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2012-06-06
    Type: Database references, Derived calculations, Non-polymer description, Other, Version format compliance