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- PDB-8hav: An auto-activation mechanism of plant non-specific phospholipase C -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hav | ||||||
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Title | An auto-activation mechanism of plant non-specific phospholipase C | ||||||
![]() | Non-specific phospholipase C4 | ||||||
![]() | HYDROLASE / NPC4 / glycosylinositolphosphorylceramide / phosphatidylcholine / phosphate | ||||||
Function / homology | ![]() phospholipase C / phosphatidylcholine phospholipase C activity / phospholipid catabolic process / phospholipase C activity / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, F. / Fan, R.Y. / Guan, Z.Y. / Guo, L. / Yin, P. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 225.5 KB | Display | ![]() |
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PDB format | ![]() | 145.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8hawC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.982404914767, 0.028385419115, 0.184593746978), (0.0338903644883, -0.999067909191, -0.0267349213646), (0.183662806895, 0.0325204675118, -0.982451216375)Vector: -6. ...NCS oper: (Code: given Matrix: (0.982404914767, 0.028385419115, 0.184593746978), Vector: |
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Components
#1: Protein | Mass: 55774.250 Da / Num. of mol.: 2 / Mutation: K178A, K179A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.38 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Hepes, PEG 3350, Magnesium Chloride Potassium sodium tartrate tetrahydrate PH range: 7.0 - 8.0 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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→50 Å / Num. obs: 78362 / % possible obs: 99.9 % / Redundancy: 12.88 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.025 / Rrim(I) all: 0.094 / Χ2: 0.99 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 13.49 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4402 / CC1/2: 0.969 / Rpim(I) all: 0.165 / Rrim(I) all: 0.438 / Χ2: 0.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() 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: 38.25 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.480350326052 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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