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Open data
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Basic information
Entry | Database: PDB / ID: 1mog | ||||||
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Title | Crystal structure of H. salinarum dodecin | ||||||
![]() | Dodecin | ||||||
![]() | UNKNOWN FUNCTION / binding site for dimerized riboflavin / 23-symmetric dodecamer | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bieger, B. / Essen, L.-O. / Oesterhelt, D. | ||||||
![]() | ![]() Title: Crystal Structure of Halophilic Dodecin: A Novel, Dodecameric Flavin Binding Protein from Halobacterium salinarum Authors: Bieger, B. / Essen, L.-O. / 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 | ![]() | 30.5 KB | Display | ![]() |
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PDB format | ![]() | 21.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.9 KB | Display | ![]() |
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Full document | ![]() | 760 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Details | The biological assembly is a dodecamer generated from the monomer in the asymmetric unit by the operations: X,Y,Z Z,X,Y Y,Z,X -X,-Y,Z -Z,-X,Y -Y,-Z,X X,-Y,-Z Z,-X,-Y Y,-Z,-X -X,Y,-Z -Z,X,-Y -Y,Z,-X |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 7310.863 Da / Num. of mol.: 1 / Fragment: residues 10-77 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Non-polymers , 5 types, 104 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/RBF.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NA / | #4: Chemical | #5: Chemical | ChemComp-RBF / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.07 Å3/Da / Density % sol: 69.78 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 400, magnesium chloride, sodium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 12, 2000 / Details: mirrors |
Radiation | Monochromator: mirrors / 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. all: 14027 / Num. obs: 14027 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 38.3 |
Reflection shell | Resolution: 1.7→1.72 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.6 / % possible all: 99.9 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 116286 |
Reflection shell | *PLUS % possible obs: 99.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.0684 Å2 / ksol: 0.445967 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→14.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 9 % / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.214 |