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- PDB-7js5: Phospholipase D engineered mutant (TNYR) inactive enzyme (H168A) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7js5 | ||||||
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Title | Phospholipase D engineered mutant (TNYR) inactive enzyme (H168A) bound to 1-inositol phosphate | ||||||
![]() | Phospholipase D | ||||||
![]() | LIPID BINDING PROTEIN / engineered mutant / pseudo-dimeric architecture / myo-inositol specificity | ||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / phospholipase D / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / lipid catabolic process / extracellular region / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vrielink, A. / Samantha, A. | ||||||
![]() | ![]() Title: Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation. Authors: Samantha, A. / Damnjanovic, J. / Iwasaki, Y. / Nakano, H. / Vrielink, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.4 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.7 KB | Display | ![]() |
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Full document | ![]() | 764.5 KB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 30 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7jrbC ![]() 7jrcC ![]() 7jruC ![]() 7jrvC ![]() 7jrwC ![]() 7js7C ![]() 2ze4S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 53848.844 Da / Num. of mol.: 1 / Fragment: UNP residues 48-556 / Mutation: V107S,H168A,G186T,W187N,A211R,Y385R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-IPD / |
#3: Chemical | ChemComp-MES / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6 / Details: 15% PEG6000, 100 mM MES, pH 6.0 |
-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: Jun 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953724 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→48.19 Å / Num. obs: 17538 / % possible obs: 99.94 % / Redundancy: 13.6 % / Biso Wilson estimate: 42.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1744 / Net I/σ(I): 14.38 |
Reflection shell | Resolution: 2.2→2.279 Å / Rmerge(I) obs: 2.066 / Num. unique obs: 2516 / CC1/2: 0.723 / % possible all: 99.72 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ZE4 Resolution: 2.5→48.19 Å / SU ML: 0.3082 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6747 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: 45.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→48.19 Å
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Refine LS restraints |
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LS refinement shell |
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