+Open data
-Basic information
Entry | Database: PDB / ID: 6tjd | |||||||||||||||
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Title | Crystal structure of the computationally designed Cake4 protein | |||||||||||||||
Components | Cake4 | |||||||||||||||
Keywords | DE NOVO PROTEIN / Beta-propeller / computationally designed / symmetrical / repeat protein | |||||||||||||||
Biological species | synthetic construct (others) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||||||||
Authors | Laier, I. / Mylemans, B. / 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 | 6tjd.cif.gz | 83.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tjd.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 6tjd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tjd_validation.pdf.gz | 429.5 KB | Display | wwPDB validaton report |
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Full document | 6tjd_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 6tjd_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 6tjd_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/6tjd ftp://data.pdbj.org/pub/pdb/validation_reports/tj/6tjd | HTTPS FTP |
-Related structure data
Related structure data | 6tjbC 6tjcC 6tjeC 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: 17610.350 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) #2: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.23 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 0.18M Magnesium acetate, 0.09M Sodium, Cacodylate pH 6.5, 27% MPD, 15% Glycerol |
-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: May 18, 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: 2.1→48.31 Å / Num. obs: 18944 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.13 Å2 / CC1/2: 0.953 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.071 / Χ2: 0.93 / Net I/σ(I): 1.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 7 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1561 / CC1/2: 0.953 / Rpim(I) all: 0.186 / Rrim(I) all: 0.497 / Χ2: 0.94 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Cake8 model Resolution: 2.1→35.6 Å / SU ML: 0.243 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.5972 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: 34.43 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→35.6 Å
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Refine LS restraints |
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LS refinement shell |
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