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Open data
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Basic information
Entry | Database: PDB / ID: 4b2m | |||||||||
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Title | COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS | |||||||||
![]() | DODECIN | |||||||||
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Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Staudt, H. / Hoesl, M. / Dreuw, A. / Serdjukow, S. / Oesterhelt, D. / Budisa, N. / Wachtveitl, J. / Grininger, M. | |||||||||
![]() | ![]() Title: The flavoprotein dodecin as a redox probe for electron transfer through DNA. Authors: Yu, Y. / Heidel, B. / Parapugna, T.L. / Wenderhold-Reeb, S. / Song, B. / Schonherr, H. / Grininger, M. / Noll, G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 31.6 KB | Display | ![]() |
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PDB format | ![]() | 21.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4b2hC ![]() 2cccS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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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: 8514.200 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TRYPTOPHAN 36 EXCHANGED BY 4AZATRYPTOPHAN, RIBOFLAVIN BOUND Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 76 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | ![]() #5: Chemical | ChemComp-SO4 / | ![]() #6: Chemical | ChemComp-RBF / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66 % / Description: NONE |
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Crystal grow![]() | pH: 7.5 Details: 0.1 M HEPES (PH 7.5), PEG 400 30% (V/V), 2.5 M NACL, 0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→20 Å / Num. obs: 8867 / % possible obs: 99.8 % / Observed criterion σ(I): 4 / Redundancy: 13.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.2 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2CCC Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.288 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.392 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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