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- PDB-6r8k: 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: 6r8k | ||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with an engineered HMA domain of Pikp-1 from rice (Oryza sativa) | ||||||||||||||||||
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![]() | PLANT PROTEIN / NLR / Complex / HMA / Rice blast | ||||||||||||||||||
Function / homology | ![]() defense response to other organism / ADP binding / ATP hydrolysis activity / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | De la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Protein engineering expands the effector recognition profile of a rice NLR immune receptor. Authors: De la Concepcion, J.C. / Franceschetti, M. / MacLean, D. / Terauchi, R. / Kamoun, S. / Banfield, M.J. #1: ![]() Title: Protein engineering expands the effector recognition profile of a rice NLR immune receptor Authors: De la Concepcion, J.C. / Franceschetti, M. / Terauchi, R. / Kamoun, S. / 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 | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 33.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 434.9 KB | Display | ![]() |
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Full document | ![]() | 435.4 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r8mC ![]() 6g10S 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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Unit cell |
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Components
#1: Protein | Mass: 8388.819 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Pi-km1, Pikh-1 / Production host: ![]() ![]() |
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#2: Protein | Mass: 10827.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2- Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1M Buffer system 1 (1M Imidazole, MES monohydrate ...Details: 0.12M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2- Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1M Buffer system 1 (1M Imidazole, MES monohydrate (acid)) pH 6.5, 50% v/v Precipitant mix 4 (25%v/v MPD, 25%v/v PEG 1000, 25%v/v PEG3350) |
-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: Apr 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→32.8 Å / Num. obs: 20294 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.024 / Rrim(I) all: 0.084 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 978 / CC1/2: 0.866 / Rpim(I) all: 0.38 / Rrim(I) all: 1.01 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6G10 Resolution: 1.6→32.8 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.987 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.56 Å2 / Biso mean: 25.609 Å2 / Biso min: 13.3 Å2
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Refinement step | Cycle: final / Resolution: 1.6→32.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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