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Yorodumi- PDB-6fub: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fub | ||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with the HMA domain of Pikm-1 from rice (Oryza sativa) | ||||||||||||||||||
Components |
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Keywords | ANTIFUNGAL PROTEIN / Plant NLR / fungal effector / Plant immunity / Complex | ||||||||||||||||||
Function / homology | Function and homology information response to other organism / ADP binding / defense response / ATP binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Magnaporthe oryzae (rice blast fungus) Oryza sativa subsp. japonica (Japanese rice) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||||||||||||||
Authors | Franceschetti, M. / De la Concepcion, J.C. / Banfield, M.J. | ||||||||||||||||||
Funding support | United Kingdom, Japan, 5items
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Citation | Journal: Nat Plants / Year: 2018 Title: Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen. Authors: De la Concepcion, J.C. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Terauchi, R. / Kamoun, S. / Banfield, M.J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fub.cif.gz | 89.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fub.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/6fub ftp://data.pdbj.org/pub/pdb/validation_reports/fu/6fub | HTTPS FTP |
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-Related structure data
Related structure data | 6fu9C 6fudC 6g10C 6g11C 5a6wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10803.295 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8C2 |
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#2: Protein | Mass: 8547.963 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Pikm1-TS, Pi-km1 / Production host: Escherichia coli (E. coli) / References: UniProt: B5UBC1 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Amino acids (0.2M L-Na-Glutamate; 0.2M Alanine (racemic); 0.2M Glycine; 0.2M Lysine HCl (racemic); 0.2M Serine (racemic)); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; ...Details: 0.1M Amino acids (0.2M L-Na-Glutamate; 0.2M Alanine (racemic); 0.2M Glycine; 0.2M Lysine HCl (racemic); 0.2M Serine (racemic)); 0.1M Buffer system 2 (1M sodium HEPES, MOPS (acid)) pH 7.5; 50% v/v Precipitant mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→23.7 Å / Num. obs: 38170 / % possible obs: 99.4 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 1.3→1.32 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A6W Resolution: 1.3→23.7 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.265 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.049 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.377 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→23.7 Å
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Refine LS restraints |
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