[English] 日本語
![](img/lk-miru.gif)
- PDB-5to4: Phospholipase C gamma-1 C-terminal SH2 domain, spacegroup P212121 -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5to4 | ||||||
---|---|---|---|---|---|---|---|
Title | Phospholipase C gamma-1 C-terminal SH2 domain, spacegroup P212121 | ||||||
![]() | 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1 | ||||||
![]() | HYDROLASE / SH2 / Phospholipase | ||||||
Function / homology | ![]() calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / phospholipid catabolic process / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / COP9 signalosome / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / cellular response to vascular endothelial growth factor stimulus / release of sequestered calcium ion into cytosol ...calcium-dependent phospholipase C activity / phosphoinositide phospholipase C / phospholipid catabolic process / phosphatidylinositol metabolic process / phosphatidylinositol phospholipase C activity / COP9 signalosome / positive regulation of epithelial cell migration / phosphatidylinositol-mediated signaling / cellular response to vascular endothelial growth factor stimulus / release of sequestered calcium ion into cytosol / cellular response to epidermal growth factor stimulus / ruffle / guanyl-nucleotide exchange factor activity / epidermal growth factor receptor signaling pathway / ruffle membrane / lamellipodium / in utero embryonic development / calcium ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wuttke, D.S. / McKercher, M.A. | ||||||
![]() | ![]() Title: Multimodal Recognition of Diverse Peptides by the C-Terminal SH2 Domain of Phospholipase C-gamma 1 Protein. Authors: McKercher, M.A. / Guan, X. / Tan, Z. / Wuttke, D.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 413.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 415 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tnwC ![]() 5tq1C ![]() 5tqsC ![]() 4k44S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 11989.685 Da / Num. of mol.: 1 / Fragment: UNP residues 663-759 Source method: isolated from a genetically manipulated source Details: Scattered electron density was also present for at least two additional polymers, likely low molecular weight polyethylene glycol molecules. However, the molecules could not be fit into the ...Details: Scattered electron density was also present for at least two additional polymers, likely low molecular weight polyethylene glycol molecules. However, the molecules could not be fit into the density non-ambiguously and were consequently omitted from the model. Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P08487, phosphoinositide phospholipase C |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.01 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium citrate (pH 5.5), 22% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→36.44 Å / Num. all: 12342 / Num. obs: 12342 / % possible obs: 97.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.08 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.092 / Rsym value: 0.084 / Net I/av σ(I): 4.706 / Net I/σ(I): 12.8 / Num. measured all: 80381 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4K44 Resolution: 1.7→28.114 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.84
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.19 Å2 / Biso mean: 29.6369 Å2 / Biso min: 10.26 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→28.114 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
|