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Open data
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Basic information
Entry | Database: PDB / ID: 6r1e | ||||||
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Title | Structure of dodecin from Streptomyces coelicolor | ||||||
![]() | dodecin | ||||||
![]() | FLAVOPROTEIN / flavin storage / dodecamer / protein complex | ||||||
Function / homology | ![]() Dodecin / Dodecin-like superfamily / Dodecin / Flavin-binding protein dodecin / Dodecin-like / Dodecin subunit-like / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Essen, L.-O. / Sander, B. | ||||||
![]() | ![]() Title: Comparative biochemical and structural analysis of the flavin-binding dodecins fromStreptomyces davaonensisandStreptomyces coelicolorreveals striking differences with regard to multimerization. Authors: Bourdeaux, F. / Ludwig, P. / Paithankar, K. / Sander, B. / Essen, L.O. / Grininger, M. / Mack, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.4 KB | Display | ![]() |
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PDB format | ![]() | 62.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ri3C ![]() 2yizS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 15 - 84 / Label seq-ID: 2 - 71
NCS ensembles :
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 7920.802 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N-formylated N-terminus Source: (gene. exp.) ![]() Gene: SCO0915 / Plasmid: pET28a(+) / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 112 molecules ![](data/chem/img/FMN.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FMN / #3: Chemical | ChemComp-COA / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #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: 2.99 Å3/Da / Density % sol: 58.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 10% PEG4000, 0.1 M NaOAc, 0.2 M AS, 16.5 mg/mL ScDodecin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2007 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→11.9 Å / Num. all: 66956 / Num. obs: 11644 / % possible obs: 99 % / Redundancy: 5.75 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 2.6→2.64 Å / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3.72 / Num. unique obs: 549 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2YIZ Resolution: 2.6→11.86 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU B: 11.074 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 0.907 / ESU R Free: 0.307 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.755 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→11.86 Å
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Refine LS restraints |
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