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- PDB-8ctp: Crystal structure of engineered phospholipase D mutant superPLD 2-23 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ctp | ||||||||||||||||||
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Title | Crystal structure of engineered phospholipase D mutant superPLD 2-23 | ||||||||||||||||||
![]() | Phospholipase D | ||||||||||||||||||
![]() | HYDROLASE / Enzyme / phospholipase / PLD / phospholipid | ||||||||||||||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / phospholipase D / membrane Similarity search - Function | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||
![]() | Tei, R. / Bagde, S.R. / Fromme, J.C. / Baskin, J.M. | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Activity-based directed evolution of a membrane editor in mammalian cells. Authors: Tei, R. / Bagde, S.R. / Fromme, J.C. / Baskin, J.M. | ||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 228.8 KB | Display | ![]() |
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PDB format | ![]() | 147.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8ctqC ![]() 1v0yS S: Starting model for refinement 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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Components
#1: Protein | Mass: 54716.098 Da / Num. of mol.: 1 / Mutation: I130M, P245A, G328S, G381V, G406S, G429D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.15 Details: 19% PEG8000, 0.15 M lithium sulfate, citrate-NaOH, pH 4.15 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→56.05 Å / Num. obs: 36421 / % possible obs: 98.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.992 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.9→1.973 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3442 / CC1/2: 0.82 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1V0Y Resolution: 1.9→56.05 Å / SU ML: 0.2065 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2561 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→56.05 Å
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Refine LS restraints |
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LS refinement shell |
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