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Yorodumi- PDB-8haw: An auto-activation mechanism of plant non-specific phospholipase C -
+Open data
-Basic information
Entry | Database: PDB / ID: 8haw | ||||||
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Title | An auto-activation mechanism of plant non-specific phospholipase C | ||||||
Components | Non-specific phospholipase C4 | ||||||
Keywords | HYDROLASE / NPC4 / non-specific phospholipase C / glycosylinositolphosphorylceramide / phosphatidylcholine | ||||||
Function / homology | Function and homology information phospholipase C / phosphatidylcholine phospholipase C activity / phospholipid catabolic process / phospholipase C activity / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Zhao, F. / Fan, R.Y. / Guan, Z.Y. / Guo, L. / Yin, P. | ||||||
Funding support | China, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Insights into the mechanism of phospholipid hydrolysis by plant non-specific phospholipase C. Authors: Fan, R. / Zhao, F. / Gong, Z. / Chen, Y. / Yang, B. / Zhou, C. / Zhang, J. / Du, Z. / Wang, X. / Yin, P. / Guo, L. / Liu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8haw.cif.gz | 265.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8haw.ent.gz | 173.2 KB | Display | PDB format |
PDBx/mmJSON format | 8haw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ha/8haw ftp://data.pdbj.org/pub/pdb/validation_reports/ha/8haw | HTTPS FTP |
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-Related structure data
Related structure data | 8havC 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: 55854.234 Da / Num. of mol.: 2 / Mutation: K178A, K179A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NPC4, At3g03530, T21P5.5 / Plasmid: pET15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SRQ7, phospholipase C #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.32 Å3/Da / Density % sol: 46.93 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 8000, Glycerol, Potassium phosphate monobasic / PH range: 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 58086 / % possible obs: 99.9 % / Redundancy: 6.67 % / Biso Wilson estimate: 19.39 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.047 / Rrim(I) all: 0.12 / Χ2: 0.98 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 6.83 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4459 / CC1/2: 0.986 / Rpim(I) all: 0.151 / Rrim(I) all: 0.284 / Χ2: 0.92 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→39.99 Å / SU ML: 0.2004 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.383 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 25.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→39.99 Å
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Refine LS restraints |
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LS refinement shell |
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