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Yorodumi- PDB-6st9: Crystal structure of the strawberry pathogenesis-related 10 (PR-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6st9 | |||||||||
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Title | Crystal structure of the strawberry pathogenesis-related 10 (PR-10) Fra a 1.02 protein, D48R mutant | |||||||||
Components | Major strawberry allergen Fra a 1-2 | |||||||||
Keywords | ALLERGEN / Fragaria x ananassa / Fra a 1 / fruit / ripening / PR-10 | |||||||||
Function / homology | Function and homology information 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 | Fragaria ananassa (strawberry) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | |||||||||
Authors | Orozco-Navarrete, B. / Kaczmarska, Z. / Dupeux, F. / Pott, D. / Diaz Perales, A. / Casanal, A. / Marquez, J.A. / Valpuesta, V. / Merchante, C. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: J.Agric.Food Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6st9.cif.gz | 77.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6st9.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 6st9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6st9_validation.pdf.gz | 817.8 KB | Display | wwPDB validaton report |
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Full document | 6st9_full_validation.pdf.gz | 817.8 KB | Display | |
Data in XML | 6st9_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 6st9_validation.cif.gz | 20.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6st9 ftp://data.pdbj.org/pub/pdb/validation_reports/st/6st9 | HTTPS FTP |
-Related structure data
Related structure data | 6st8C 6staC 6stbC 5amwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 17762.133 Da / Num. of mol.: 2 / Mutation: D48R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Fragaria ananassa (strawberry) / Gene: FRAA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0E0C6 #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.97 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Displacement parameters | Biso mean: 49.85 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→82.4 Å
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LS refinement shell | Resolution: 1.97→2.08 Å
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