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Yorodumi- PDB-7nlj: Complex of rice blast (Magnaporthe oryzae) effector protein APikL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7nlj | |||||||||
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Title | Complex of rice blast (Magnaporthe oryzae) effector protein APikL2A with host target sHMA25 from Setaria italica | |||||||||
Components |
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Keywords | PLANT PROTEIN / complex / heavy-metal associated domain / fungal virulence protein | |||||||||
Function / homology | Heavy metal-associated isoprenylated plant protein 16/46/47 / Uncharacterized protein Function and homology information | |||||||||
Biological species | Setaria italica (foxtail millet) Pyricularia oryzae Y34 (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Bentham, A.R. / Banfield, M.J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Plos Pathog. / Year: 2021 Title: A single amino acid polymorphism in a conserved effector of the multihost blast fungus pathogen expands host-target binding spectrum. Authors: Bentham, A.R. / Petit-Houdenot, Y. / Win, J. / Chuma, I. / Terauchi, R. / Banfield, M.J. / Kamoun, S. / Langner, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7nlj.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nlj.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 7nlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nlj_validation.pdf.gz | 444.6 KB | Display | wwPDB validaton report |
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Full document | 7nlj_full_validation.pdf.gz | 445.4 KB | Display | |
Data in XML | 7nlj_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 7nlj_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/7nlj ftp://data.pdbj.org/pub/pdb/validation_reports/nl/7nlj | HTTPS FTP |
-Related structure data
Related structure data | 7nmmC 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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-Components
#1: Protein | Mass: 8352.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Setaria italica (foxtail millet) / Gene: 101766303, SETIT_7G131400v2 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle / References: UniProt: K3YAU1 | ||||
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#2: Protein | Mass: 10747.252 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyricularia oryzae Y34 (fungus) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): SHuffle | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.2 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: Morpheus well H10 Molecular Dimensions. 0.1 M Amino acids, 0.1 M Buffer System 3, 50% v/v Precipitant Mix 2 |
-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 PILATUS3 6M / Detector: PIXEL / Date: May 18, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.039 Å / Num. obs: 18505 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.99 / Rrim(I) all: 0.058 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 12.7 % / Num. unique obs: 1060 / CC1/2: 0.798 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A6w Resolution: 1.8→41.04 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.503 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.127 / 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: 109.4 Å2 / Biso mean: 44.666 Å2 / Biso min: 26.05 Å2
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Refinement step | Cycle: final / Resolution: 1.8→41.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 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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