+Open data
-Basic information
Entry | Database: PDB / ID: 8pr9 | ||||||
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Title | The structure of v13Bagel2 | ||||||
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: 2.35 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 | 8pr9.cif.gz | 133 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pr9.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pr9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8pr9 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8pr9 | HTTPS FTP |
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-Related structure data
Related structure data | 8prdC 8preC 8prfC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 9107.999 Da / Num. of mol.: 8 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 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.58 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7 / Details: 0.1 M HEPES pH 7 30% v/v Jeffamine M-600 pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→96.95 Å / Num. obs: 25904 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.035 / Rrim(I) all: 0.127 / Net I/σ(I): 8.4 / Num. measured all: 331634 |
Reflection shell | Resolution: 2.35→2.39 Å / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.816 / Num. measured all: 14219 / Num. unique obs: 1272 / CC1/2: 0.952 / Rpim(I) all: 0.254 / Rrim(I) all: 0.856 / Net I/σ(I) obs: 0.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→63.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.813 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.583 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 43.75 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→63.35 Å
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