[English] 日本語
![](img/lk-miru.gif)
- PDB-7yis: Crystal structure of N-terminal PH domain of ARAP3 protein in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7yis | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of N-terminal PH domain of ARAP3 protein in complex with inositol 1,3,4,5-tetrakisphosphate | ||||||
![]() | Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / ruffle / cytoskeleton organization / RAC1 GTPase cycle / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y.J. / Liu, Y.R. / Wu, B. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3. Authors: Zhang, Y. / Ge, L. / Xu, L. / Liu, Y. / Wang, J. / Liu, C. / Zhao, H. / Xing, L. / Wang, J. / Wu, B. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 39.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7yirC ![]() 1faoS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 13056.944 Da / Num. of mol.: 1 / Fragment: PH1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-4PT / ( |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.16 % |
---|---|
Crystal grow![]() | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Ammonium sulfate, 0.1 M Sodium acetate trihydrate (pH 4.6), 30% v/v Polyethylene glycol 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 3.297→50 Å / Num. obs: 3029 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 63.73 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 16 |
Reflection shell | Resolution: 3.297→3.36 Å / Rmerge(I) obs: 0.487 / Num. unique obs: 146 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 1FAO Resolution: 3.3→32.11 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.31 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.48 Å2 / Biso mean: 57.3664 Å2 / Biso min: 30.16 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.3→32.11 Å
| ||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 2
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 30.7448 Å / Origin y: -11.955 Å / Origin z: 3.5196 Å
| ||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: (chain 'A' and resid 286 through 383) |