+Open data
-Basic information
Entry | Database: PDB / ID: 6tje | |||||||||||||||
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Title | Crystal structure of the computationally designed Cake5 protein | |||||||||||||||
Components | Cake5 | |||||||||||||||
Keywords | DE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å | |||||||||||||||
Authors | Mylemans, B. / Laier, I. / Noguchi, H. / Voet, A.R.D. | |||||||||||||||
Funding support | Belgium, 4items
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Citation | Journal: Febs J. / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tje.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tje.ent.gz | 52.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tje.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tje_validation.pdf.gz | 419.1 KB | Display | wwPDB validaton report |
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Full document | 6tje_full_validation.pdf.gz | 419.8 KB | Display | |
Data in XML | 6tje_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 6tje_validation.cif.gz | 17 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tje ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tje | HTTPS FTP |
-Related structure data
Related structure data | 6tjbC 6tjcC 6tjdC 6tjfC 6tjgC 6tjhC 6tjiC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21905.072 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.41 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium chloride, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.15→52.72 Å / Num. obs: 12312 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 107.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.033 / Rrim(I) all: 0.119 / Χ2: 0.98 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 3.15→3.37 Å / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3074 / CC1/2: 0.961 / Rpim(I) all: 0.211 / Rrim(I) all: 0.769 / Χ2: 1.17 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Cake9 Resolution: 3.15→52.72 Å / SU ML: 0.384 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.3247 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: 121.19 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.15→52.72 Å
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Refine LS restraints |
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LS refinement shell |
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