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Open data
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Basic information
Entry | Database: PDB / ID: 8prm | ||||||
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Title | The structure of nvBagel2 binding the P8W48O184 polyoxometalate | ||||||
![]() | 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 v13Bagel2 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 | ![]() | 83.9 KB | Display | ![]() |
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PDB format | ![]() | 62.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8pr9C ![]() 8prdC ![]() 8preC ![]() 8prfC ![]() 8prgC ![]() 8prhC ![]() 8priC ![]() 8proC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 9050.947 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 35947 / DSM 3960 / H-6-12 / Gene: DICTH_0179 Production host: ![]() ![]() References: UniProt: B5YBJ6 #2: Chemical | ChemComp-IR0 / | Mass: 12016.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O184P8W48 / Feature type: SUBJECT OF INVESTIGATION #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.1 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 8 Details: 0.1 M Tris pH 8.5, 5% (w/v) PEG 6000 (final pH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97242 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→46.11 Å / Num. obs: 30774 / % possible obs: 100 % / Redundancy: 12.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.048 / Rrim(I) all: 0.164 / Χ2: 0.95 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.2→2.27 Å / % possible obs: 100 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.837 / Num. measured all: 18768 / Num. unique obs: 1382 / CC1/2: 0.951 / Rpim(I) all: 0.236 / Rrim(I) all: 0.87 / Χ2: 0.76 / Net I/σ(I) obs: 3.5 |
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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: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→39.91 Å
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Refine LS restraints |
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LS refinement shell |
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