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Open data
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Basic information
Entry | Database: PDB / ID: 8wkh | ||||||
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Title | Crystal structure of group 13 allergen from Blomia tropicalis | ||||||
![]() | Fatty acid-binding protein | ||||||
![]() | ALLERGEN / BETA BARREL / HELIX | ||||||
Function / homology | DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, K.L. / Gong, Y. / Cui, Y.B. | ||||||
Funding support | 1items
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![]() | ![]() Title: Immunobiological properties and structure analysis of group 13 allergen from Blomia tropicalis and its IgE-mediated cross-reactivity. Authors: Zhou, Y. / Zhu, K. / Li, Q. / Zhou, D. / Ren, Y. / Liao, Y. / Cao, P. / Gong, Y. / Cui, 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 | ![]() | 76.9 KB | Display | ![]() |
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PDB format | ![]() | 53.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 434.1 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 11.9 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: 14878.856 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: In the sequence, the first residue G is a expression tag. Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-TRS / |
#3: Chemical | ChemComp-PEG / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH7.5 and 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 8802 / % possible obs: 96.1 % / Redundancy: 5.2 % / Biso Wilson estimate: 34.92 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.042 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 4 / Num. unique obs: 420 / CC1/2: 0.838 / % possible all: 88.2 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.93 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30.49 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.7576 Å / Origin y: 19.9387 Å / Origin z: 12.8294 Å
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