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Open data
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Basic information
Entry | Database: PDB / ID: 2cie | ||||||
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Title | Complexes of Dodecin with Flavin and Flavin-like Ligands | ||||||
![]() | VNG1446H | ||||||
![]() | FLAVOPROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grininger, M. / Seiler, F. / Zeth, K. / Oesterhelt, D. | ||||||
![]() | ![]() Title: Dodecin Sequesters Fad in Closed Conformation from the Aqueous Solution. Authors: Grininger, M. / Seiler, F. / Zeth, K. / Oesterhelt, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 30 KB | Display | ![]() |
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PDB format | ![]() | 20.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 904 KB | Display | ![]() |
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Full document | ![]() | 904.1 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cifC ![]() 2cjcC ![]() 2cc9S 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: 7038.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: APOPROTEIN CRYSTALS SOAKED WITH FAD / 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/FAD.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-FAD / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 64.68 % |
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Crystal grow | pH: 7.5 Details: 0.2 M MGCL2, 2.0 M NACL, 0.1 M NA HEPES PH 7.5 AND 30% PEG400 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 8, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 122830 / % possible obs: 99.7 % / Observed criterion σ(I): 3.5 / Redundancy: 10.27 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.58 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 10.29 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.54 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CC9 Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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