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Open data
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Basic information
Entry | Database: PDB / ID: 4b2h | ||||||
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Title | COMPLEXES OF DODECIN WITH FLAVIN AND FLAVIN-LIKE LIGANDS | ||||||
![]() | DODECIN | ||||||
![]() | FLAVOPROTEIN / BIOTECHNOLOGICAL APPLICATION OF DODECIN BINDING PROPERTIES / FLAVIN-DNA LIGAND HYBRID | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yu, Y. / Heidel, B. / Parapugna, T.L. / Wenderhold-Reeb, S. / Song, B. / Schoenherr, H. / Grininger, M. / Noell, G. | ||||||
![]() | ![]() 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 | ![]() | 31.7 KB | Display | ![]() |
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PDB format | ![]() | 21.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.6 KB | Display | ![]() |
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Full document | ![]() | 757.2 KB | Display | |
Data in XML | ![]() | 7.1 KB | Display | |
Data in CIF | ![]() | 8.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4b2mC ![]() 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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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: 8196.948 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Details: LIGAND-BOUND FORM / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 85 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/C3F.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/C3F.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-C3F / | #5: Chemical | ChemComp-MG / | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEEREDNonpolymer details | [4-(7,8-DIMETHYL-2,4-DIOXO-3, 4-DIHYDROBENZO[G]PTERIDIN-10(2H)-YL)PROPYL]CARBAMIC ACID (C3F): ...[4-(7,8-DIMETHYL-2,4-DIOXO-3, 4-DIHYDROBEN | Sequence details | MUTATION OF E45A AND DELETION OF GLU50 AND GLU51 OE3073R AT HALOLEX DATABASE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.44 Å3/Da / Density % sol: 72.28 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 20156 / % possible obs: 99.9 % / Observed criterion σ(I): 5 / Redundancy: 18 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 18 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 5.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CCC Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.897 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 21.739 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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