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- PDB-6fu9: 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: 6fu9 | ||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikm-1 from rice (Oryza sativa) | ||||||||||||||||||
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![]() | ANTIFUNGAL PROTEIN / Plant NLR / fungal effector / Plant immunity / Complex | ||||||||||||||||||
Function / homology | ![]() defense response to other organism / ADP binding / ATP binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Franceschetti, M. / De la Concepcion, J.C. / Banfield, M.J. | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 156.1 KB | Display | ![]() |
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PDB format | ![]() | 123.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6fubC ![]() 6fudC ![]() 6g10C ![]() 6g11C ![]() 5a6wS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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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: 8547.963 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: Pikm1-TS, Pi-km1 / Production host: ![]() ![]() #2: Protein | Mass: 10827.340 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene-glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol); 0.1M Buffer system 3 (1M Tris (base); BICINE) pH 8.5; 50% v/v ...Details: 0.12M Ethylene glycols (0.3M Diethylene glycol; 0.3M Triethylene-glycol; 0.3M Tetraethylene glycol; 0.3M Pentaethylene glycol); 0.1M Buffer system 3 (1M Tris (base); BICINE) pH 8.5; 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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9168 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→29.04 Å / Num. obs: 104301 / % possible obs: 98.5 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.2→1.23 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A6W Resolution: 1.2→29.04 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.588 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.039 / 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: 22.92 Å2
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Refinement step | Cycle: 1 / Resolution: 1.2→29.04 Å
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Refine LS restraints |
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