+Open data
-Basic information
Entry | Database: PDB / ID: 8prf | ||||||
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Title | The structure of nvBagel5 | ||||||
Components | Cell surface protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Protein design / symmetric / assembly / self-assembly / beta-propeller | ||||||
Function / homology | Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Vandebroek, L. / Voet, A.R.D. / Lee, X.Y. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: The structure of v13Bagel2 Authors: Vandebroek, L. / Voet, A.R.D. / Lee, X.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8prf.cif.gz | 29.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8prf.ent.gz | 17.2 KB | Display | PDB format |
PDBx/mmJSON format | 8prf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8prf ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8prf | HTTPS FTP |
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-Related structure data
Related structure data | 8pr9C 8prdC 8preC 8prgC 8prhC 8priC 8prmC 8proC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 9050.947 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Gene: DICTH_0179 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B5YBJ6 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.61 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8 Details: 0.2M ZnAcetate, 0.1M Imidazole pH8.0, 25% 1-2 propanol, 10% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 3, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87313 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50.02 Å / Num. obs: 2374 / % possible obs: 100 % / Redundancy: 34.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.049 / Rrim(I) all: 0.291 / Χ2: 1.02 / Net I/σ(I): 25.1 / Num. measured all: 81171 |
Reflection shell | Resolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 36.9 % / Rmerge(I) obs: 0.603 / Num. measured all: 12335 / Num. unique obs: 334 / CC1/2: 0.994 / Rpim(I) all: 0.1 / Rrim(I) all: 0.611 / Χ2: 0.98 / Net I/σ(I) obs: 12.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.73 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 15.79 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→39.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→39.73 Å
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