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Open data
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Basic information
Entry | Database: PDB / ID: 7arr | ||||||
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Title | The de novo designed hybrid alpha/beta-miniprotein | ||||||
![]() | alpha/beta-peptide | ||||||
![]() | DE NOVO PROTEIN / alpha/beta-peptide / foldamer | ||||||
Function / homology | trifluoroacetic acid![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bejger, M. / Fortuna, P. / Drewniak-Switalska, M. / Rypniewski, W. / Berlicki, L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A computationally designed beta-amino acid-containing miniprotein. Authors: Bejger, M. / Fortuna, P. / Drewniak-Switalska, M. / Plewka, J. / Rypniewski, W. / Berlicki, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 89.2 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7arsC C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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Links
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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/peptide | Mass: 4081.618 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #2: Chemical | ChemComp-TFA / | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M magnesium chloride hexahydrate 0.1 M HEPES pH 7.5 25 % w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→50 Å / Num. obs: 49390 / % possible obs: 87.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.027 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.1→1.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 7.34 / Num. unique obs: 7297 / CC1/2: 0.98 / % possible all: 80.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: not deposited Resolution: 1.1→29.02 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 1.174 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 101.16 Å2 / Biso mean: 14.162 Å2 / Biso min: 6.17 Å2
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Refinement step | Cycle: final / Resolution: 1.1→29.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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