[English] 日本語
![](img/lk-miru.gif)
- PDB-1jo8: Structural analysis of the yeast actin binding protein Abp1 SH3 domain -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1jo8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural analysis of the yeast actin binding protein Abp1 SH3 domain | ||||||
![]() | ACTIN BINDING PROTEIN | ||||||
![]() | STRUCTURAL PROTEIN / SH3 domain Actin-binding-protein | ||||||
Function / homology | ![]() protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / site of polarized growth / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding ...protein localization to actin cortical patch / positive regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch assembly / site of polarized growth / actin cortical patch / regulation of actin filament polymerization / mating projection tip / barbed-end actin filament capping / cortical actin cytoskeleton / actin filament binding / cell cortex / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fazi, B. / Cope, M.J. / Douangamath, A. / Ferracuti, S. / Schirwitz, K. / Zucconi, A. / Drubin, D.G. / Wilmanns, M. / Cesareni, G. / Castagnoli, L. | ||||||
![]() | ![]() Title: Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis. Authors: Fazi, B. / Cope, M.J. / Douangamath, A. / Ferracuti, S. / Schirwitz, K. / Zucconi, A. / Drubin, D.G. / Wilmanns, M. / Cesareni, G. / Castagnoli, L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 41.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 30.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 431.4 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ckaS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 6663.082 Da / Num. of mol.: 1 / Fragment: SH3 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: pRSETA / Production host: ![]() ![]() | ||
---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.6 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: Ammonium sulfate, bis-tris-propane, pH 8.0, VAPOR DIFFUSION, SITTING DROP at 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 2000 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.842 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→25 Å / Num. all: 57575 / Num. obs: 56424 / % possible obs: 98 % / Redundancy: 4.1 % / Biso Wilson estimate: 9.8 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.266 / Mean I/σ(I) obs: 4 / Num. unique all: 617 / % possible all: 88.6 |
Reflection | *PLUS Lowest resolution: 40 Å / Num. obs: 13742 / % possible obs: 98 % / Num. measured all: 56424 |
Reflection shell | *PLUS % possible obs: 88.6 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 1CKA Resolution: 1.3→17.51 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.742 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→17.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.3→1.334 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.194 / Rfactor Rwork: 0.171 / Total num. of bins used: 20 |