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Yorodumi- PDB-3wwa: Crystal structure of the computationally designed Pizza7 protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wwa | ||||||
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Title | Crystal structure of the computationally designed Pizza7 protein after heat treatment | ||||||
Components | Pizza7H protein | ||||||
Keywords | DE NOVO PROTEIN / Computational protein design / Self-assembly | ||||||
Function / homology | TolB, C-terminal domain / 6 Propeller / Neuraminidase / Mainly Beta / ISOPROPYL ALCOHOL Function and homology information | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.988 Å | ||||||
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. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wwa.cif.gz | 58 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wwa.ent.gz | 41.9 KB | Display | PDB format |
PDBx/mmJSON format | 3wwa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ww/3wwa ftp://data.pdbj.org/pub/pdb/validation_reports/ww/3wwa | HTTPS FTP |
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-Related 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: 30123.080 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The protein was designed. |
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#2: Chemical | ChemComp-IPA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085M HEPES Sodium Salt pH 7.5, 8.5% Isopropanol, 17% PEG 4000, 15% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 19, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.988→50 Å / Num. obs: 17958 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 39.27 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 8.69 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.988→34.704 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 27.17 / Stereochemistry target values: ML
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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: 1.988→34.704 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: 6
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