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Yorodumi- PDB-6kz8: Crystal structure of plant Phospholipase D alpha complex with pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kz8 | |||||||||||||||||||||
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Title | Crystal structure of plant Phospholipase D alpha complex with phosphatidic acid | |||||||||||||||||||||
Components | Phospholipase D alpha 1 | |||||||||||||||||||||
Keywords | HYDROLASE / Phospholipase D / calcium activation / C2 domain / phosphatidic acid / inhibitor | |||||||||||||||||||||
Function / homology | Function and homology information leaf shaping / positive regulation of abscisic acid-activated signaling pathway / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase activity / seed germination / ethylene-activated signaling pathway / phospholipase D activity / regulation of stomatal movement / phospholipid catabolic process ...leaf shaping / positive regulation of abscisic acid-activated signaling pathway / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase activity / seed germination / ethylene-activated signaling pathway / phospholipase D activity / regulation of stomatal movement / phospholipid catabolic process / phosphatidylcholine metabolic process / response to abscisic acid / plasmodesma / abscisic acid-activated signaling pathway / vacuole / clathrin-coated vesicle / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / chloroplast / fatty acid metabolic process / mitochondrial membrane / calcium ion binding / endoplasmic reticulum / mitochondrion / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.291 Å | |||||||||||||||||||||
Authors | Li, J.X. / Yu, F. / Zhang, P. | |||||||||||||||||||||
Funding support | China, 6items
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Citation | Journal: Cell Res. / Year: 2020 Title: Crystal structure of plant PLD alpha 1 reveals catalytic and regulatory mechanisms of eukaryotic phospholipase D. Authors: Li, J. / Yu, F. / Guo, H. / Xiong, R. / Zhang, W. / He, F. / Zhang, M. / Zhang, P. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kz8.cif.gz | 331.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kz8.ent.gz | 267 KB | Display | PDB format |
PDBx/mmJSON format | 6kz8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kz/6kz8 ftp://data.pdbj.org/pub/pdb/validation_reports/kz/6kz8 | HTTPS FTP |
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-Related structure data
-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: 91967.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PLDALPHA1, PLD1, At3g15730, MSJ11.13 / Production host: Escherichia coli (E. coli) / References: UniProt: Q38882, phospholipase D #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 3000, 0.1M Tris-HCl (pH 7.0), 0.2M Ca(OAc)2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→37.89 Å / Num. obs: 101062 / % possible obs: 99.8 % / Redundancy: 12.6 % / CC1/2: 0.992 / Net I/σ(I): 27.6 |
Reflection shell | Resolution: 2.3→2.37 Å / Num. unique obs: 6209 / CC1/2: 0.785 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.291→37.89 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.74 / 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: 80.69 Å2 / Biso mean: 15.7814 Å2 / Biso min: 1.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.291→37.89 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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