+Open data
-Basic information
Entry | Database: PDB / ID: 6tjf | |||||||||||||||
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Title | Crystal structure of the computationally designed Cake6 protein | |||||||||||||||
Components | Cake6 | |||||||||||||||
Keywords | DE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||||||||
Authors | Mylemans, B. / Laier, I. / Voet, A.R.D. / Noguchi, H. | |||||||||||||||
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 | 6tjf.cif.gz | 303.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tjf.ent.gz | 225.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tjf_validation.pdf.gz | 461.4 KB | Display | wwPDB validaton report |
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Full document | 6tjf_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 6tjf_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 6tjf_validation.cif.gz | 70.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjf ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjf | HTTPS FTP |
-Related structure data
Related structure data | 6tjbC 6tjcC 6tjdC 6tjeC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26199.795 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.35 Å3/Da / Density % sol: 47.59 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium sulfate, 0.1M Tris pH 8.5, 25% PEG5000MME |
-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: 2.4→57.05 Å / Num. obs: 54166 / % possible obs: 98.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 46.97 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.033 / Rrim(I) all: 0.062 / Χ2: 0.52 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.4→2.47 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4459 / CC1/2: 0.907 / Rpim(I) all: 0.0235 / Rrim(I) all: 0.453 / Χ2: 0.61 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Cake9 crystal structure Resolution: 2.4→57.05 Å / SU ML: 0.3249 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.3629 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: 48.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→57.05 Å
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Refine LS restraints |
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LS refinement shell |
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