[English] 日本語
Yorodumi- PDB-7a8w: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a8w | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikC with an engineered HMA domain of Pikp-1 from rice (Oryza sativa) | ||||||||||||||||||
Components |
| ||||||||||||||||||
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: 2.15 Å | ||||||||||||||||||
Authors | Maidment, J.H.R. / De la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J. | ||||||||||||||||||
Funding support | United Kingdom, 5items
| ||||||||||||||||||
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. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7a8w.cif.gz | 183.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7a8w.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a8w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a8/7a8w ftp://data.pdbj.org/pub/pdb/validation_reports/a8/7a8w | HTTPS FTP |
---|
-Related structure data
Related structure data | 7a8xC 5a6wS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8622.131 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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.17 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→44.165 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|