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Open data
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Basic information
Entry | Database: PDB / ID: 2ccc | ||||||
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Title | Complexes of Dodecin with Flavin and Flavin-like Ligands | ||||||
![]() | VNG1446H | ||||||
![]() | FLAVOPROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Grininger, M. / Zeth, K. / Oesterhelt, D. | ||||||
![]() | ![]() Title: Dodecins: A Family of Lumichrome Binding Proteins. Authors: Grininger, M. / 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 | ![]() | 29.3 KB | Display | ![]() |
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PDB format | ![]() | 20.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 711.3 KB | Display | ![]() |
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Full document | ![]() | 711.6 KB | Display | |
Data in XML | ![]() | 6.4 KB | Display | |
Data in CIF | ![]() | 8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2cc6SC ![]() 2cc7C ![]() 2cc8C ![]() 2cc9C ![]() 2ccbC 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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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: 7442.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: LUMIFLAVIN BOUND / Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 6 types, 86 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LFN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/LFN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-LFN / | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.08 Å3/Da / Density % sol: 69.85 % |
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Crystal grow | pH: 7.5 Details: 2 M NACL, 0.2 M MGCL2, 0.1 M NA, HEPES 30% (W/V), PEG400, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2004 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 22864 / % possible obs: 99.7 % / Observed criterion σ(I): 3.8 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2CC6 Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.408 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.074 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.77 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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