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Yorodumi- PDB-7a8x: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a8x | ||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with the HMA domain of Pikh-1 from rice (Oryza sativa) | ||||||||||||||||||
Components |
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Keywords | ANTIFUNGAL PROTEIN / Fungal effector / HMA domain / NLR protein / MAX effector | ||||||||||||||||||
Function / homology | Function and homology information defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) Magnaporthe oryzae (rice blast fungus) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||||||||
Authors | Maidment, J.H.R. / Xiao, G. / Franceschetti, M. / Banfield, M.J. | ||||||||||||||||||
Funding support | United Kingdom, 5items
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Citation | Journal: Plos Pathog. / Year: 2021 Title: The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface. Authors: De la Concepcion, J.C. / Maidment, J.H.R. / Longya, A. / Xiao, G. / Franceschetti, M. / Banfield, M.J. #1: Journal: Biorxiv / Year: 2020 Title: The allelic rice immune receptor Pikh confers extended resistance to strains of the blast fungus through a single polymorphism in the effector binding interface Authors: De la Concepcion, J.C. / Maidment, J.H.R. / Longya, A. / Xiao, G. / Franceschetti, M. / 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 | 7a8x.cif.gz | 176.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a8x.ent.gz | 137.7 KB | Display | PDB format |
PDBx/mmJSON format | 7a8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/7a8x ftp://data.pdbj.org/pub/pdb/validation_reports/a8/7a8x | HTTPS FTP |
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-Related structure data
Related structure data | 7a8wSC 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: 8234.721 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Pi-km1, Pikh-1 / Production host: Escherichia coli (E. coli) / References: UniProt: D5L9G5 #2: Protein | Mass: 10847.306 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (strain 70-15 / ATCC MYA-4617 / FGSC 8958) (fungus) Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_15972 / Production host: Escherichia coli (E. coli) / References: UniProt: G4MXW3 #3: Water | ChemComp-HOH / | |
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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: 2.68 Å3/Da / Density % sol: 54.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 1 (1 M Imidazole; MES monohydrate ...Details: 0.12 M Monosaccharides (0.2M D-Glucose; 0.2M D-Mannose; 0.2M D-Galactose; 0.2M L-Fucose; 0.2M D-Xylose; 0.2M N-Acetyl-D-Glucosamine); 0.1 M Buffer system 1 (1 M Imidazole; MES monohydrate (acid)) pH 6.5; 50% v/v Precipitant mix 1 (40% v/v PEG 500; MME; 20 % w/v PEG 20000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2017 | |||||||||||||||||||||||||||
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.3→107.84 Å / Num. obs: 25847 / % possible obs: 96.4 % / Redundancy: 13.1 % / CC1/2: 1 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 22.7 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7A8W Resolution: 2.3→65.922 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 14.014 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.295 / ESU R Free: 0.232 Details: Hydrogens have been added in their 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 / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.185 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→65.922 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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