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Open data
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Basic information
Entry | Database: PDB / ID: 8prt | ||||||
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Title | The structure of nvBagel8 in the presence of Co(II) | ||||||
![]() | Cell surface protein | ||||||
![]() | BIOSYNTHETIC PROTEIN / Protein design / symmetric / assembly / self-assembly / beta-propeller | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vandebroek, L. / Voet, A.R.D. / Lee, X.Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The structure of nvBagel8 in the presence of Co(II) Authors: Vandebroek, L. / Voet, A.R.D. / Lee, X.Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 62.9 KB | Display | ![]() |
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PDB format | ![]() | 46 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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 Details: nvBagel8 / Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: B5YBJ6 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.49 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 6.5 Details: 0.0085 M Cobalt chloride, 0.085 M MES pH 6.5, 1.53 M Ammonium sulfate, 15 %(v/v) Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97629 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.59 Å / Num. obs: 19762 / % possible obs: 100 % / Redundancy: 23 % / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.02 / Rrim(I) all: 0.094 / Χ2: 0.89 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 1.65→1.68 Å / % possible obs: 100 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.723 / Num. measured all: 10921 / Num. unique obs: 510 / CC1/2: 0.978 / Rpim(I) all: 0.157 / Rrim(I) all: 0.74 / Χ2: 0.68 / Net I/σ(I) obs: 4.4 |
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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: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.59 Å
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Refine LS restraints |
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LS refinement shell |
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