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Open data
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Basic information
Entry | Database: PDB / ID: 2vkg | ||||||
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Title | COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS | ||||||
![]() | DODECIN | ||||||
![]() | ELECTRON TRANSPORT / BIOTECHNOLOGICAL APPLICATION OF DODECIN BINDING PROPERTIES / FLAVIN-DNA LIGAND HYBRID | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grininger, M. / Noell, G. / Trawoeger, S. / Sinner, E. / Oesterhelt, D. | ||||||
![]() | ![]() Title: Electrochemical Switching of the Flavoprotein Dodecin at Gold Surfaces Modified by Flavin-DNA Hybrid Linkers Authors: Grininger, M. / Noell, G. / Trawoeger, S. / Sinner, E. / Oesterhelt, D. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30.1 KB | Display | ![]() |
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PDB format | ![]() | 20.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 694.4 KB | Display | ![]() |
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Full document | ![]() | 695.4 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vkfC ![]() 2cccS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 6722.342 Da / Num. of mol.: 1 / Fragment: RESIDUES 11-58,61-74 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LIGAND BOUND / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 92 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CF4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CF4.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CF4 / [ | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDNonpolymer details | COFC4_O5 (CF4): SYNTHETIC FLAVIN | Sequence details | MUTATION OF E45A AND DELETION OF GLU50,GLU51(UNP GLU59, GLU60) | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 64.82 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.2 M MGCL2, 2 M NACL, 0.1 M HEPES, 30% PEG400, PH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 20, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 107589 / % possible obs: 97.1 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.4 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CCC Resolution: 1.8→19.75 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.948 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CRYSTALS WERE SOAKED WITH A FLAVIN-DNA HYBRID LIGAND. JUST THE ISOALLOXAZINE PART AS WELL AS THE ALIPHATIC PART IS VISIBLE IN DENSITY. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CRYSTALS WERE SOAKED WITH A FLAVIN-DNA HYBRID LIGAND. JUST THE ISOALLOXAZINE PART AS WELL AS THE ALIPHATIC PART IS VISIBLE IN DENSITY. BASES ARE NOT INCLUDED IN THE MODEL FOR THE LIGAND, BUT CAUSE SOME NOT EXPLAINED DENSITY IN BINDING POCKET.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→19.75 Å
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Refine LS restraints |
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