2VKF

COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS

PDB DOI: https://doi.org/10.2210/pdb2VKF/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Halobacterium salinarum R1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-12-19 Released: 2008-09-30
Deposition Author(s): Grininger, M., Noell, G., Trawoeger, S., Sinner, E., Oesterhelt, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213
R-Value Work: 0.184
R-Value Observed: 0.186

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 20408700 Search on PubMed
DOI: https://doi.org/10.1116/1.2965134
Primary Citation of Related Structures:
2VKF, 2VKG

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 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.

Macromolecule Content

Total Structure Weight: 7.5 kDa
Atom Count: 621
Modelled Residue Count: 62
Deposited Residue Count: 62
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DODECIN	A	62	Halobacterium salinarum R1	Mutation(s): 1
UniProt
Find proteins for Q9HPW4 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore Q9HPW4 Go to UniProtKB: Q9HPW4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HPW4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CF2 Query on CF2 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth 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		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213
R-Value Work: 0.184
R-Value Observed: 0.186
Space Group: F 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.704	α = 90
b = 141.704	β = 90
c = 141.704	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-09-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-09-30
Type: Initial release
Version 1.1: 2012-06-06
Changes: Database references, Derived calculations, Non-polymer description, Other, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description