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Yorodumi- PDB-6g10: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g10 | ||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikp-1 from rice (Oryza sativa) | ||||||||||||||||||
Components |
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Keywords | ANTIFUNGAL PROTEIN / Plant NLR / fungal effector / Plant immunity / Complex | ||||||||||||||||||
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: 1.35 Å | ||||||||||||||||||
Authors | De la Concepcion, J.C. / Franceschetti, M. / Banfield, M.J. | ||||||||||||||||||
Funding support | United Kingdom, Japan, 5items
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Citation | Journal: Nat Plants / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6g10.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6g10.ent.gz | 87.6 KB | Display | PDB format |
PDBx/mmJSON format | 6g10.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g1/6g10 ftp://data.pdbj.org/pub/pdb/validation_reports/g1/6g10 | HTTPS FTP |
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-Related structure data
Related structure data | 6fu9C 6fubC 6fudC 6g11C 5a6wS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 188 - 257 / Label seq-ID: 5 - 74
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-Components
#1: Protein | Mass: 8373.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Gene: Pikp-1 / Production host: Escherichia coli DH1 (bacteria) / References: UniProt: E9KPB5 #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 DH1 (bacteria) / References: UniProt: C4B8B8 #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 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 |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→42 Å / Num. obs: 48646 / % possible obs: 99.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.35→1.37 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A6W Resolution: 1.35→42 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.897 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.053 / 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: 23.14 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→42 Å
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Refine LS restraints |
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