[English] 日本語
Yorodumi- PDB-6r8k: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r8k | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with an engineered HMA domain of Pikp-1 from rice (Oryza sativa) | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | PLANT PROTEIN / NLR / Complex / HMA / Rice blast | ||||||||||||||||||
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: 1.6 Å | ||||||||||||||||||
Authors | De la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J. | ||||||||||||||||||
Funding support | United Kingdom, Japan, 5items
| ||||||||||||||||||
Citation | Journal: Elife / Year: 2019 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: Journal: Biorxiv / Year: 2019 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6r8k.cif.gz | 49.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6r8k.ent.gz | 33.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/6r8k ftp://data.pdbj.org/pub/pdb/validation_reports/r8/6r8k | HTTPS FTP |
---|
-Related structure data
Related structure data | 6r8mC 6g10S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 8388.819 Da / Num. of mol.: 1 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: 10827.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Magnaporthe oryzae (rice blast fungus) / Gene: AVR-Pik, AvrPik, Pikm, Pikp / Production host: Escherichia coli (E. coli) / References: UniProt: C4B8B8 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 36.01 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→32.8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|