[English] 日本語
![](img/lk-miru.gif)
- PDB-7jru: Phospholipase D engineered mutant bound to phosphatidic acid (8 h... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7jru | ||||||
---|---|---|---|---|---|---|---|
Title | Phospholipase D engineered mutant bound to phosphatidic acid (8 hour soak) | ||||||
![]() | Phospholipase D | ||||||
![]() | HYDROLASE / engineered mutant / pseudo-dimeric architecture / myo-inositol specificity | ||||||
Function / homology | ![]() cardiolipin synthase activity / cardiolipin biosynthetic process / N-acylphosphatidylethanolamine-specific phospholipase D activity / phospholipase D activity / phospholipase D / 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 113.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7jrbC ![]() 7jrcC ![]() 7jrvC ![]() 7jrwC ![]() 7js5C ![]() 7js7C ![]() 2ze4S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54002.027 Da / Num. of mol.: 1 / Fragment: UNP residues 48-556 / Mutation: V107S,G186T,W187N,A211R,Y385R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MES / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-VHY / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.78 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 20, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→48.13 Å / Num. obs: 25322 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.2 / Net I/σ(I): 10.13 |
Reflection shell | Resolution: 2.21→2.29 Å / Num. unique obs: 2472 / CC1/2: 0.782 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2ZE4 Resolution: 2.21→48.13 Å / Cross valid method: FREE R-VALUE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.87 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→48.13 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.21→2.29 Å
|