[English] 日本語
![](img/lk-miru.gif)
- PDB-2y8f: Structure of the Ran-binding domain from human RanBP3 (wild type) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2y8f | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the Ran-binding domain from human RanBP3 (wild type) | ||||||
![]() | RAN-BINDING PROTEIN 3 | ||||||
![]() | PROTEIN TRANSPORT / CRM1-MEDIATED NUCLEAR EXPORT | ||||||
Function / homology | ![]() R-SMAD binding / nuclear pore / protein export from nucleus / GTPase activator activity / small GTPase binding / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Langer, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C. | ||||||
![]() | ![]() Title: Insights Into the Function of the Crm1 Cofactor Ranbp3 from the Structure of its Ran-Binding Domain Authors: Langer, K. / Dian, C. / Rybin, V. / Muller, C.W. / Petosa, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 203.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 164 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 472.2 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 31.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 15547.807 Da / Num. of mol.: 4 / Fragment: RAN BINDING DOMAIN, RESIDUES 320-454 Source method: isolated from a genetically manipulated source Details: ISOFORM3 / Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CL / | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Sequence details | GAM REMAINING RESIDUES FROM TEV CLEAVAGE SITE | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % / Description: NONE |
---|---|
Crystal grow | pH: 7.5 / Details: 30% PEG 3350, 50 MM TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 10, 2009 / Details: TOROIDAL MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48 Å / Num. obs: 33296 / % possible obs: 100 % / Observed criterion σ(I): 4 / Redundancy: 5.6 % / Biso Wilson estimate: 27.51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-
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 / Bsol: 58.181 Å2 / ksol: 0.385 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.72 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→44.399 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|