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- PDB-6stb: Crystal structure of the strawberry pathogenesis-related 10 (PR-1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6stb | |||||||||
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Title | Crystal structure of the strawberry pathogenesis-related 10 (PR-10) Fra a 1.02 protein, Q64W mutant | |||||||||
![]() | Major strawberry allergen Fra a 1-2 | |||||||||
![]() | ALLERGEN / Fragaria x ananassa / Fra a 1 / fruit / ripening / PR-10 | |||||||||
Function / homology | ![]() flavonoid biosynthetic process / response to biotic stimulus / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / defense response / signaling receptor activity / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Orozco-Navarrete, B. / Kaczmarska, Z. / Dupeux, F. / Pott, D. / Diaz Perales, A. / Casanal, A. / Marquez, J.A. / Valpuesta, V. / Merchante, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Bases for the Allergenicity of Fra a 1.02 in Strawberry Fruits. Authors: Orozco-Navarrete, B. / Kaczmarska, Z. / Dupeux, F. / Garrido-Arandia, M. / Pott, D. / Perales, A.D. / Casanal, A. / Marquez, J.A. / Valpuesta, V. / Merchante, C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.6 KB | Display | ![]() |
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PDB format | ![]() | 54.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.5 KB | Display | ![]() |
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Full document | ![]() | 426.6 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6st8C ![]() 6st9C ![]() 6staC ![]() 5amwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 17778.107 Da / Num. of mol.: 2 / Mutation: Q64W Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH5.5 200 mM Magnesium chloride 26.5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.267→54.201 Å / Num. obs: 10544 / % possible obs: 90.5 % / Redundancy: 5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.06 / Rrim(I) all: 0.14 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.267→2.531 Å / Rmerge(I) obs: 1.241 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 528 / CC1/2: 0.615 / Rpim(I) all: 0.504 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5AMW Resolution: 2.27→44.08 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.901 / SU R Cruickshank DPI: 1.055 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.657 / SU Rfree Blow DPI: 0.322 / SU Rfree Cruickshank DPI: 0.323
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Displacement parameters | Biso mean: 51.47 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→44.08 Å
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LS refinement shell | Resolution: 2.27→2.49 Å
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