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Yorodumi- PDB-5cy5: Crystal structure of the T33-51H designed self-assembling protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cy5 | ||||||
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Title | Crystal structure of the T33-51H designed self-assembling protein tetrahedron | ||||||
Components |
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Keywords | DE NOVO PROTEIN / BIONANOTECHNOLOGY / SYMMETRY / BIOMATERIALS / TETRAHEDRAL / COMPUTATIONAL DESIGN / ROSETTA / SELF-ASSEMBLY / NANOMATERIAL / SOLUBILITY | ||||||
Function / homology | Hypothetical Protein Ta1238; Chain: A; / Cobalamin adenosyltransferase-like / Up-down Bundle / Mainly Alpha Function and homology information | ||||||
Biological species | Thermoplasma acidophilum (acidophilic) Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.4 Å | ||||||
Authors | Cannon, K.A. / Cascio, D. / Park, R. / Boyken, S. / King, N. / Yeates, T.O. | ||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Design and structure of two new protein cages illustrate successes and ongoing challenges in protein engineering. Authors: Cannon, K.A. / Park, R.U. / Boyken, S.E. / Nattermann, U. / Yi, S. / Baker, D. / King, N.P. / Yeates, T.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5cy5.cif.gz | 127.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cy5.ent.gz | 99.2 KB | Display | PDB format |
PDBx/mmJSON format | 5cy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/5cy5 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/5cy5 | HTTPS FTP |
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-Related structure data
Related structure data | 5vl4C 1nogS 1wy1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 21031.225 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) |
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#2: Protein | Mass: 19344.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET29b / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.94 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8.8 / Details: 100 mM HEPES pH 8.8 and 15 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.4→75.448 Å / Num. obs: 5827 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge F obs: 1 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.094 / Χ2: 0.992 / Net I/σ(I): 29.04 / Num. measured all: 154895 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1nog, 1wy1 Resolution: 3.4→75.448 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.18 / Stereochemistry target values: TWIN_LSQ_F
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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 max: 150.48 Å2 / Biso mean: 81.1072 Å2 / Biso min: 42.68 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.4→75.448 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 90 %
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Refinement TLS params. | Method: refined / Origin x: 32.276 Å / Origin y: -31.569 Å / Origin z: -0.238 Å
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Refinement TLS group |
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