[English] 日本語
![](img/lk-miru.gif)
- PDB-6st9: Crystal structure of the strawberry pathogenesis-related 10 (PR-1... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6st9 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the strawberry pathogenesis-related 10 (PR-10) Fra a 1.02 protein, D48R mutant | |||||||||
![]() | Major strawberry allergen Fra a 1-2 | |||||||||
![]() | ALLERGEN / Fragaria x ananassa / Fra a 1 / fruit / ripening / PR-10 | |||||||||
Function / homology | ![]() flavonoid biosynthetic process / 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 | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 77.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6st8C ![]() 6staC ![]() 6stbC ![]() 5amwS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17762.133 Da / Num. of mol.: 2 / Mutation: D48R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Bis-Tris pH5.5 200 mM Ammonium Sulfate 34% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
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: 1.97→82.4 Å / Num. obs: 19595 / % possible obs: 91.6 % / Redundancy: 4.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.032 / Rrim(I) all: 0.071 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.97→2.139 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.209 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 980 / CC1/2: 0.451 / Rpim(I) all: 0.569 / % possible all: 59.5 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5AMW Resolution: 1.97→82.4 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.24 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.247 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.207
| ||||||||||||||||||||
Displacement parameters | Biso mean: 49.85 Å2
| ||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→82.4 Å
| ||||||||||||||||||||
LS refinement shell | Resolution: 1.97→2.08 Å
|