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- PDB-3wwf: Crystal structure of the computationally designed Pizza2-SR protein -
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Open data
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Basic information
Entry | Database: PDB / ID: 3wwf | ||||||
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Title | Crystal structure of the computationally designed Pizza2-SR protein | ||||||
![]() | pizza2sr-pb protein | ||||||
![]() | DE NOVO PROTEIN / Computational protein design / Self-assembly | ||||||
Function / homology | Thrombin, subunit H - #500 / Thrombin, subunit H / Beta Barrel / Mainly Beta![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Voet, A.R.D. / Noguchi, H. / Addy, C. / Simoncini, D. / Terada, D. / Unzai, S. / Park, S.Y. / Zhang, K.Y.J. / Tame, J.R.H. | ||||||
![]() | ![]() Title: Computational design of a self-assembling symmetrical beta-propeller protein. Authors: Voet, A.R.D. / Noguchi, H. / Addy, C. / Simoncini, D. / Terada, D. / Unzai, S. / Park, S.Y. / Zhang, K.Y.J. / Tame, J.R.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 58.1 KB | Display | ![]() |
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PDB format | ![]() | 43.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.8 KB | Display | ![]() |
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Full document | ![]() | 432.1 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9143.111 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: The protein was designed. #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1M Lithium Chloride, 0.1M Tris-HCl pH 8.0, 20% PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 35121 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 64.88 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 19.32 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.601→28.864 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: 13
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