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Yorodumi- PDB-5amw: Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5amw | ||||||
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Title | Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 2 protein (A141F) processed with the CrystalDirect automated mounting and cryo-cooling technology | ||||||
Components | Fra a 2 allergen | ||||||
Keywords | ALLERGEN / PYR/PYL/RCAR / BET V 1 / FLAVONOIDS / AUTOMATED CRYSTAL HARVESTING / AUTOMATED CRYO-COOLING / CRYSTALDIRECT | ||||||
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 / OTHER / Resolution: 1.9 Å | ||||||
Authors | Zander, U. / Casanal, A. / Pott, D. / Valpuesta, V. / Hoffmann, G. / Cornaciu, I. / Cipriani, F. / Marquez, J.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Automated Harvesting and Processing of Protein Crystals Through Laser Photoablation. Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / ...Authors: Zander, U. / Hoffmann, G. / Cornaciu, I. / Marquette, J.-P. / Papp, G. / Landret, C. / Seroul, G. / Sinoir, J. / Roewer, M. / Felisaz, F. / Rodriguez-Puente, S. / Mariaule, V. / Murphy, P. / Mathieu, M. / Cipriani, F. / Marquez, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5amw.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5amw.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 5amw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/5amw ftp://data.pdbj.org/pub/pdb/validation_reports/am/5amw | HTTPS FTP |
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-Related structure data
Related structure data | 5amxC 5amzC 5an4C 5andC 5aneC 5angC 5aniC 5anjC 5ankC 5anlC 5anoC 5dwpC 5ebhC 5an2 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.2541, 0.0207, 0.967), Vector: |
-Components
#1: Protein | Mass: 17739.070 Da / Num. of mol.: 2 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.68 % / Description: NONE |
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Crystal grow | Details: 0.1 M BIS-TRIS,PH=5.5, 0.2 M AMMONIUM SULFATE, 25% PEG 3350, |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Type: ESRF / Wavelength: 0.9763 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. obs: 28520 / % possible obs: 99.9 % / Observed criterion σ(I): 2.2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.08 |
-Processing
Software | Name: REFMAC / Version: 5.8.0123 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.868 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES, REFINED INDIVIDUALLY
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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: 35.023 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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