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Yorodumi- PDB-7xvk: Modularity of Phytophthora effectors enables host mimicry of a pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xvk | |||||||||
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Title | Modularity of Phytophthora effectors enables host mimicry of a principal phosphatase | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / plant immunology / translocation / effector / phosphatase | |||||||||
Function / homology | Function and homology information protein phosphatase type 2A complex / protein phosphatase regulator activity / regulation of phosphorylation / protein dephosphorylation / peroxisome / host cell / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) Phytophthora sojae (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | |||||||||
Authors | Wang, J. / Wang, Y. | |||||||||
Funding support | China, 2items
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Citation | Journal: Cell / Year: 2023 Title: Pathogen protein modularity enables elaborate mimicry of a host phosphatase. Authors: Li, H. / Wang, J. / Kuan, T.A. / Tang, B. / Feng, L. / Wang, J. / Cheng, Z. / Sklenar, J. / Derbyshire, P. / Hulin, M. / Li, Y. / Zhai, Y. / Hou, Y. / Menke, F.L.H. / Wang, Y. / Ma, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xvk.cif.gz | 232.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xvk.ent.gz | 179.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xvk_validation.pdf.gz | 840.2 KB | Display | wwPDB validaton report |
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Full document | 7xvk_full_validation.pdf.gz | 862.9 KB | Display | |
Data in XML | 7xvk_validation.xml.gz | 46.9 KB | Display | |
Data in CIF | 7xvk_validation.cif.gz | 69.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xvk ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xvk | HTTPS FTP |
-Related structure data
Related structure data | 7xviC 2nppS 5gncS 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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Unit cell |
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-Components
#1: Protein | Mass: 43547.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PP2AA2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38950 | ||||
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#2: Protein | Mass: 68382.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phytophthora sojae (eukaryote) / Gene: PSR2 / Production host: Escherichia coli (E. coli) / References: UniProt: E0W4V5 | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.68 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 5% PEG 20000 0.1 M Bis tris pH 5.8 5 mM MgSO4 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 9, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.29→50 Å / Num. obs: 62511 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Χ2: 0.932 / Net I/σ(I): 8.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5GNC,2NPP Resolution: 2.29→38.77 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.72 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.07 Å2 / Biso mean: 39.5009 Å2 / Biso min: 5.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.29→38.77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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