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- PDB-7a8w: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a8w | ||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with an engineered HMA domain of Pikp-1 from rice (Oryza sativa) | ||||||||||||||||||
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![]() | ANTIFUNGAL PROTEIN / Fungal effector / HMA domain / NLR protein / MAX effector | ||||||||||||||||||
Function / homology | ![]() defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Maidment, J.H.R. / De la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.4 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.8 KB | Display | ![]() |
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Full document | ![]() | 469.6 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a8xC ![]() 5a6wS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 8622.131 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Pi-km1, Pikh-1 / Production host: ![]() ![]() #2: Protein | Mass: 10847.306 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 70-15 / ATCC MYA-4617 / FGSC 8958 / Gene: MGG_15972 / Production host: ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 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 2 (Sodium HEPES; MOPS (acid)) pH 7.5; ...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 2 (Sodium HEPES; MOPS (acid)) pH 7.5; 37.5% v/v Precipitant mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.17 Å / Num. obs: 31604 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.015 / Rrim(I) all: 0.055 / Net I/σ(I): 23.9 |
Reflection shell | Resolution: 2.15→2.22 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2694 / CC1/2: 0.925 / Rpim(I) all: 0.278 / Rrim(I) all: 1.034 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A6W Resolution: 2.15→44.165 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 7.997 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.204 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: 63.54 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→44.165 Å
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Refine LS restraints |
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