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Yorodumi- PDB-7b1i: Complex of rice blast (Magnaporthe oryzae) effector protein AVR-P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b1i | ||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikF with the HMA domain of OsHIPP19 from rice (Oryza sativa) | ||||||
Components |
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Keywords | PLANT PROTEIN / complex / effector / HMA domain / rice / rice blast fungus | ||||||
Function / homology | Heavy metal-associated isoprenylated plant protein 47 / Avr-Pik / AVR-Pik protein / OSIGBa0128P10.9 protein Function and homology information | ||||||
Biological species | Oryza sativa (Asian cultivated rice) Magnaporthe oryzae (rice blast fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Maidment, J.H.R. / Franceschetti, M. / Banfield, M.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Multiple variants of the fungal effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19, providing a foundation to engineer plant defense. Authors: Maidment, J.H.R. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Jantasuriyarat, C. / Kamoun, S. / Terauchi, R. / Banfield, M.J. #1: Journal: Biorxiv / Year: 2020 Title: Multiple variants of the blast fungus effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19 with high affinity Authors: Maidment, J.H.R. / Franceschetti, M. / Maqbool, A. / Saitoh, H. / Jantasuriyarat, C. / Kamoun, S. / Terauchi, R. / 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 | 7b1i.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b1i.ent.gz | 57.7 KB | Display | PDB format |
PDBx/mmJSON format | 7b1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/7b1i ftp://data.pdbj.org/pub/pdb/validation_reports/b1/7b1i | HTTPS FTP |
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-Related structure data
Related structure data | 5a6wS 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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-Components
#1: Protein | Mass: 8337.907 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa (Asian cultivated rice) / Gene: OSIGBa0150F01.4, OSIGBa0128P10.9 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01IL6 |
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#2: Protein | Mass: 10856.250 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, UniProt: A0A219T3Y8*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.86 % |
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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 3 pH 8.5 [1M Tris (base); BICINE], ...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 3 pH 8.5 [1M Tris (base); BICINE], 50% v/v Precipitant Mix 1 [40% v/v PEG 500* MME; 20% w/v PEG 20000] |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→98.03 Å / Num. obs: 13077 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.038 / Rrim(I) all: 0.135 / Net I/σ(I): 12.4 / Num. measured all: 165357 | ||||||||||||||||||||||||||||||
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: 1.9→98.03 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 7.897 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.146 / 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: 82.19 Å2 / Biso mean: 37.001 Å2 / Biso min: 17.14 Å2
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Refinement step | Cycle: final / Resolution: 1.9→98.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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