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- PDB-6y7n: The crystal structure of the eight-bladed symmetrical designer pr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6y7n | ||||||
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Title | The crystal structure of the eight-bladed symmetrical designer protein Tako8 in the presence of tellurotungstic Anderson-Evans (TEW) | ||||||
![]() | Tako8 | ||||||
![]() | DE NOVO PROTEIN / Designer protein / polyoxometalate / POM / TEW / packing | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vandebroek, L. / Noguchi, H. / Parac-Vogt, T.N. / Van Meervelt, L. / Voet, A.R.D. | ||||||
![]() | ![]() Title: Shape and Size Complementarity-Induced Formation of Supramolecular Protein Assemblies with Metal-Oxo Clusters Authors: Vandebroek, L. / Noguchi, H. / Kamata, K. / Tame, J.R.H. / Parac-Vogt, T.N. / Voet, A.R.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 | ![]() | 143.6 KB | Display | ![]() |
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PDB format | ![]() | 111 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.6 KB | Display | ![]() |
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Full document | ![]() | 427.1 KB | Display | |
Data in XML | ![]() | 26.9 KB | Display | |
Data in CIF | ![]() | 42 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6y7oC ![]() 6y7pC ![]() 6g6mS 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
#1: Protein | Mass: 35024.230 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.5 / Details: 0.1M sodium acetate, 3.1M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.94 Å / Num. obs: 85806 / % possible obs: 99.8 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.025 / Rpim(I) all: 0.023 / Rrim(I) all: 0.033 / Net I/σ(I): 21.4 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 8.3 / Num. unique obs: 4215 / CC1/2: 0.994 / Rpim(I) all: 0.07 / Rrim(I) all: 0.103 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6g6m Resolution: 1.6→46.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 37.65
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 81.51 Å2 / Biso mean: 19.4706 Å2 / Biso min: 5.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→46.93 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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