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Open data
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Basic information
Entry | Database: PDB / ID: 6j98 | ||||||
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Title | Crystal structure of P8 from Lactobacillus rhamnosus | ||||||
![]() | P8 | ||||||
![]() | UNKNOWN FUNCTION / Lactobacillus Rhamnosus / P8 | ||||||
Function / homology | Uncharacterized protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cha, Y.J. / Cho, H.S. | ||||||
![]() | ![]() Title: Crystal structure of P8 from Lactobacillus rhamnosus Authors: Cha, Y.J. / Cho, H.S. #1: Journal: Toxicol Res / Year: 2014 Title: A Probiotic Preparation Duolac-Gold Ameliorates Dextran Sulphate Sodium-induced Mouse Colitis by Downregulating the Expression of IL-6. Authors: Yoon, H. / Yoon, Y.S. / Kim, M.S. / Chung, M.J. / Yum, D.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 | ![]() | 28.6 KB | Display | ![]() |
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PDB format | ![]() | 20.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.1 KB | Display | ![]() |
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Full document | ![]() | 417.1 KB | Display | |
Data in XML | ![]() | 6.2 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 9188.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: B4Q13_10920, BGK71_11245, CCE29_09795, DBP98_10520, PY66_06245, PY91_09235 Production host: ![]() ![]() | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.39 % |
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Crystal grow | Temperature: 290 K / Method: microbatch Details: 0.05M Zinc Acetate dihydrate, 20% PEG3350, 5% n-dodecyl-N, N-dimethylamine-N-oxide |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 17, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9738 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→38.17 Å / Num. obs: 12894 / % possible obs: 99.7 % / Redundancy: 20 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 4.95 |
Reflection shell | Resolution: 1.56→1.601 Å / Rmerge(I) obs: 0.6 / Num. unique obs: 925 / Rpim(I) all: 0.18 / % possible all: 98.98 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 16.651 Å2
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Refinement step | Cycle: 1 / Resolution: 1.56→38.17 Å
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Refine LS restraints |
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