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Yorodumi- PDB-7qzd: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qzd | ||||||||||||||||||||||||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with an engineered HMA domain of Pikp-1 (Pikp-SNK-EKE) from rice (Oryza sativa) | ||||||||||||||||||||||||||||||
Components |
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Keywords | ANTIFUNGAL PROTEIN / Plant immunity / pathogen effector / protein engineering / blast disease | ||||||||||||||||||||||||||||||
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 Japonica Group (Japanese rice) Pyricularia oryzae (rice blast fungus) | ||||||||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||||||||||||||||||||
Authors | Maidment, J.H.R. / Franceschetti, M. / Longya, A. / Banfield, M.J. | ||||||||||||||||||||||||||||||
Funding support | Japan, 9items
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Citation | Journal: Elife / Year: 2023 Title: Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor. Authors: Maidment, J.H.R. / Shimizu, M. / Bentham, A.R. / Vera, S. / Franceschetti, M. / Longya, A. / Stevenson, C.E.M. / De la Concepcion, J.C. / Bialas, A. / Kamoun, S. / Terauchi, R. / Banfield, M.J. #1: Journal: Biorxiv / Year: 2022 Title: Effector target-guided engineering of an integrated domain expands the disease resistance profile of a rice NLR immune receptor Authors: Maidment, J. / Shimizu, M. / Vera, S. / Franceschetti, M. / Longya, A. / Stevenson, C. / De la Concepcion, J. / Bialas, A. / Kamoun, S. / Terauchi, R. / Banfield, M. | ||||||||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qzd.cif.gz | 190.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qzd.ent.gz | 152.1 KB | Display | PDB format |
PDBx/mmJSON format | 7qzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qzd_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 7qzd_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 7qzd_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 7qzd_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/7qzd ftp://data.pdbj.org/pub/pdb/validation_reports/qz/7qzd | HTTPS FTP |
-Related structure data
Related structure data | 7qpxC 5a6wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 8430.855 Da / Num. of mol.: 4 / Mutation: S258E, N261K, K262E Source method: isolated from a genetically manipulated source Details: expressed protein corresponds to residues 186-263 of wild type sequence. N-terminal GP is a scar from the cleaved expression tag Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Gene: Pikp-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E9KPB5 #2: Protein | Mass: 10833.278 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: expressed protein corresponds to residues 22-113 of wild type sequence. N-terminal M was added. Source: (gene. exp.) Pyricularia oryzae (rice blast fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A219T3Y8 #3: 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: 2.5 Å3/Da / Density % sol: 50.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 14, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→103.8 Å / Num. obs: 28553 / % possible obs: 97.4 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.038 / Rrim(I) all: 0.105 / Net I/σ(I): 11.5 / Num. measured all: 195704 / Scaling rejects: 28 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A6W Resolution: 2.2→63.83 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2758 / WRfactor Rwork: 0.2169 / FOM work R set: 0.731 / SU B: 17.721 / SU ML: 0.214 / SU R Cruickshank DPI: 0.2819 / SU Rfree: 0.2367 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.282 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.56 Å2 / Biso mean: 42.021 Å2 / Biso min: 19.77 Å2
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Refinement step | Cycle: final / Resolution: 2.2→63.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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