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- PDB-7ymr: Complex structure of lysoplasmalogen specific phopholipase D, F21... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ymr | ||||||
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Title | Complex structure of lysoplasmalogen specific phopholipase D, F211L mutant with LPC | ||||||
![]() | Lysoplasmalogenase | ||||||
![]() | HYDROLASE / phospholipase D / lysoplasalogen / lysoPAF / LPC | ||||||
Function / homology | Glycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / metal ion binding / Chem-KIP / Lysoplasmalogenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Murayama, K. / Kato-Murayama, M. / Sugimori, D. / Shirouzu, M. / Hamana, H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural basis for the substrate specificity switching of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. RD004668. Authors: Hamana, H. / Yasutake, Y. / Kato-Murayama, M. / Hosaka, T. / Shirouzu, M. / Sakasegawa, S.I. / Sugimori, D. / Murayama, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 260.8 KB | Display | ![]() |
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PDB format | ![]() | 193.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 45.3 KB | Display | |
Data in CIF | ![]() | 60.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ym0C ![]() 7ympC ![]() 7ymqC ![]() 2pz0S 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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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34418.059 Da / Num. of mol.: 4 / Mutation: F211L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-KIP / [( #3: 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: 4.72 Å3/Da / Density % sol: 73.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Sodium Chloride, HEPES, Ammonium Sulfate, LPC |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Jul 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→49.56 Å / Num. obs: 73238 / % possible obs: 99.9 % / Redundancy: 29.6 % / Biso Wilson estimate: 81.2 Å2 / CC1/2: 1 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 2.69→2.75 Å / Num. unique obs: 4425 / CC1/2: 0.568 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2pz0 Resolution: 2.69→48.38 Å / SU ML: 0.3814 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3518 / Stereochemistry target values: GeoStd + Monomer Library
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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: 83.67 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.69→48.38 Å
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Refine LS restraints |
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LS refinement shell |
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