[English] 日本語
Yorodumi- PDB-8pq7: The Potato Late Blight pathogen (Phytophthora infestans) effector... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pq7 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The Potato Late Blight pathogen (Phytophthora infestans) effector protein Pi04134 in complex with potato protein phosphatase type 1c (PP1c). | |||||||||||||||
Components |
| |||||||||||||||
Keywords | PLANT PROTEIN / protein complex / plant pathogen interactions / effector protein / phosphatase | |||||||||||||||
Function / homology | Function and homology information host cell nucleoplasm / host cell nucleolus / myosin phosphatase activity / protein-serine/threonine phosphatase / extracellular region Similarity search - Function | |||||||||||||||
Biological species | Solanum tuberosum (potato) Phytophthora infestans (potato late blight agent) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||||||||
Authors | Bentham, A.R. / Banfield, M.J. | |||||||||||||||
Funding support | United Kingdom, 4items
| |||||||||||||||
Citation | Journal: Mol.Plant Microbe Interact. / Year: 2024 Title: The WY Domain of an RxLr Effector Drives Interactions with a Host Target Phosphatase to Mimic Host Regulatory Proteins and Promote Phytophthora infestans Infection. Authors: Bentham, A.R. / Wang, W. / Trusch, F. / Varden, F.A. / Birch, P.R.J. / Banfield, M.J. | |||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8pq7.cif.gz | 312 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8pq7.ent.gz | 252.2 KB | Display | PDB format |
PDBx/mmJSON format | 8pq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pq7_validation.pdf.gz | 469.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8pq7_full_validation.pdf.gz | 482.9 KB | Display | |
Data in XML | 8pq7_validation.xml.gz | 30.8 KB | Display | |
Data in CIF | 8pq7_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/8pq7 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/8pq7 | HTTPS FTP |
-Related structure data
Related structure data | 5inbS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33600.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solanum tuberosum (potato) / Gene: 102587690 / Production host: Escherichia coli (E. coli) / References: UniProt: M1C5B8 #2: Protein | Mass: 10450.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora infestans (potato late blight agent) Gene: PexRD24, PITG_04314 / Production host: Escherichia coli (E. coli) / References: UniProt: D0N0Z8 #3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % |
---|---|
Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium fluoride, 0.1 M BIS-TRIS propose pH 8.5, 20 % PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91188 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Nov 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91188 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→58.62 Å / Num. obs: 40927 / % possible obs: 97.6 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rrim(I) all: 0.097 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 3300 / CC1/2: 0.84 / Rrim(I) all: 0.527 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5INB Resolution: 2.1→58.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 14.158 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 40.062 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→58.62 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|