[English] 日本語
![](img/lk-miru.gif)
- PDB-2ihs: Crystal structure of the B30.2/SPRY domain of GUSTAVUS in complex... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ihs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the B30.2/SPRY domain of GUSTAVUS in complex with a 20-residue VASA peptide | ||||||
![]() |
| ||||||
![]() | PEPTIDE BINDING PROTEIN / B30.2/SPRY / GUSTAVUS / VASA / SPRY-containing SOCS box / F-box-SPRY / TRIM family | ||||||
Function / homology | ![]() cuticle pattern formation / Neddylation / oocyte anterior/posterior axis specification / pole plasm / secondary piRNA processing / posterior cell cortex / Antigen processing: Ubiquitination & Proteasome degradation / wing disc morphogenesis / pole plasm assembly / dorsal appendage formation ...cuticle pattern formation / Neddylation / oocyte anterior/posterior axis specification / pole plasm / secondary piRNA processing / posterior cell cortex / Antigen processing: Ubiquitination & Proteasome degradation / wing disc morphogenesis / pole plasm assembly / dorsal appendage formation / gamete generation / germ cell migration / elongin complex / P granule / Cul5-RING ubiquitin ligase complex / germ cell nucleus / SCF ubiquitin ligase complex / oogenesis / germ cell development / positive regulation of protein catabolic process / protein localization / cell cortex / proteasome-mediated ubiquitin-dependent protein catabolic process / RNA helicase activity / cell differentiation / intracellular signal transduction / RNA helicase / mRNA binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Woo, J.S. / Park, S.Y. / Oh, B.H. | ||||||
![]() | ![]() Title: Structural Basis for Protein Recognition by B30.2/SPRY Domains Authors: Woo, J.S. / Suh, H.Y. / Park, S.Y. / Oh, B.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 76.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 2fnjS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 24180.625 Da / Num. of mol.: 2 / Fragment: B30.2/SPRY domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 2497.696 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P09052, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% (w/v) PEG 8000, 0.2M calcium acetate, 0.1M imidazole (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD / Date: Feb 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 27426 / Num. obs: 26376 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.036 / Net I/σ(I): 37.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2143 / Rsym value: 0.224 / % possible all: 79.9 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDP ENTRY 2FNJ Resolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.23 Å
|