[English] 日本語
![](img/lk-miru.gif)
- PDB-4rv3: Crystal structure of a pentafluoro-Phe incorporated Phosphatidyli... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4rv3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a pentafluoro-Phe incorporated Phosphatidylinositol-specific phospholipase C (H258X)from Staphylococcus aureus | ||||||
![]() | 1-phosphatidylinositol phosphodiesterase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | He, T. / Gershenson, A. / Eyles, S.J. / Gao, J. / Roberts, M.F. | ||||||
![]() | ![]() Title: Fluorinated Aromatic Amino Acids Distinguish Cation-pi Interactions from Membrane Insertion. Authors: He, T. / Gershenson, A. / Eyles, S.J. / Lee, Y.J. / Liu, W.R. / Wang, J. / Gao, J. / Roberts, M.F. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 72.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34296.055 Da / Num. of mol.: 1 / Mutation: H258(PF5) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P45723, ![]() |
---|---|
#2: Chemical | ChemComp-ACT / ![]() |
#3: Chemical | ChemComp-INS / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % |
---|---|
Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 26% PEG 4000,0.150M ammonium acetate,0.1M sodium acetate, 0.1M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 28, 2014 |
Radiation | Monochromator: Osmic VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2→49.87 Å / Num. all: 23089 / Num. obs: 22311 / % possible obs: 96.61 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.31 % |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.9 / % possible all: 74.6 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.87 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|