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Open data
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Basic information
Entry | Database: PDB / ID: 6tjc | |||||||||||||||
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Title | Crystal structure of the computationally designed Cake3 protein | |||||||||||||||
![]() | Cake3 | |||||||||||||||
![]() | DE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein | |||||||||||||||
Function / homology | PHOSPHATE ION![]() | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Laier, I. / Mylemans, B. / Voet, A.R.D. / Noguchi, H. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural plasticity of a designer protein sheds light on beta-propeller protein evolution. Authors: Mylemans, B. / Laier, I. / Kamata, K. / Akashi, S. / Noguchi, H. / Tame, J.R.H. / 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 | ![]() | 94.1 KB | Display | ![]() |
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PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
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Full document | ![]() | 442.4 KB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6tjbC ![]() 6tjdC ![]() 6tjeC ![]() 6tjfC ![]() 6tjgC ![]() 6tjhC ![]() 6tjiC 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
#1: Protein | Mass: 13315.628 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: ![]() ![]() #2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.05M Potassium phosphate, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 26, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.36 Å / Num. obs: 28542 / % possible obs: 100 % / Redundancy: 8.6 % / Biso Wilson estimate: 28 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.02 / Rrim(I) all: 0.059 / Χ2: 0.95 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 5.6 / Num. unique obs: 1793 / CC1/2: 0.957 / Rpim(I) all: 0.132 / Rrim(I) all: 0.409 / Χ2: 0.78 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Computational design Resolution: 1.9→46.36 Å / SU ML: 0.1529 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6721 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→46.36 Å
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Refine LS restraints |
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LS refinement shell |
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