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- PDB-8ctq: Crystal structure of engineered phospholipase D mutant superPLD 2-48 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ctq | ||||||||||||||||||
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Title | Crystal structure of engineered phospholipase D mutant superPLD 2-48 | ||||||||||||||||||
![]() | Phospholipase D | ||||||||||||||||||
![]() | HYDROLASE / Enzyme / phospholipase / PLD / phospholipid | ||||||||||||||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / 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 | ![]() | 231.3 KB | Display | ![]() |
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PDB format | ![]() | 148.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 934.2 KB | Display | ![]() |
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Full document | ![]() | 938.1 KB | Display | |
Data in XML | ![]() | 21.2 KB | Display | |
Data in CIF | ![]() | 31.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ctpC ![]() 1v0yS C: citing same article ( S: Starting model for refinement |
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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: 54796.168 Da / Num. of mol.: 1 Mutation: K57R, A59V, K109R, P245A, V264I, 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: 39 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.4 Details: 21% PEG8000, 0.15 M lithium sulfate, citrate-NaOH, pH 4.4 |
-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: 1.85→56.09 Å / Num. obs: 40025 / % possible obs: 99.15 % / Redundancy: 13.1 % / Biso Wilson estimate: 28.98 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.55 |
Reflection shell | Resolution: 1.85→1.918 Å / Mean I/σ(I) obs: 2.35 / Num. unique obs: 3612 / CC1/2: 0.879 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1V0Y Resolution: 1.85→56.09 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.1422 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: 36.66 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→56.09 Å
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Refine LS restraints |
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LS refinement shell |
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