+Open data
-Basic information
Entry | Database: PDB / ID: 8pra | ||||||
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Title | The structure of v13Bagel4 | ||||||
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: 2.05 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 v13Bagel4 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 | 8pra.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pra.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 8pra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pra_validation.pdf.gz | 454.8 KB | Display | wwPDB validaton report |
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Full document | 8pra_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 8pra_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 8pra_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/8pra ftp://data.pdbj.org/pub/pdb/validation_reports/pr/8pra | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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: 17727.473 Da / Num. of mol.: 4 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: 2.21 Å3/Da / Density % sol: 44.24 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 Details: 0.14 M tri-Sodium citrate 0.07 M Sodium cacodylate pH 6.5 21 %(v/v) Isopropanol 30 %(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→83.5 Å / Num. obs: 40133 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.029 / Rrim(I) all: 0.091 / Net I/σ(I): 7.9 / Num. measured all: 373426 |
Reflection shell | Resolution: 2.05→2.09 Å / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.741 / Num. measured all: 18576 / Num. unique obs: 1981 / CC1/2: 0.847 / Rpim(I) all: 0.246 / Rrim(I) all: 0.782 / Net I/σ(I) obs: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→63.47 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 36.28 / Stereochemistry target values: MLHL
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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: 2.05→63.47 Å
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Refine LS restraints |
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LS refinement shell |
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