+
Open data
-
Basic information
Entry | Database: PDB / ID: 5d78 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of RRM3 Domain of Mip6 at 1.25 A Resolution | ||||||
![]() | RNA-binding protein MIP6 | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() mRNA localization resulting in post-transcriptional regulation of gene expression / mRNA metabolic process / prospore membrane / ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mohamad, N. / Bravo, J. | ||||||
![]() | ![]() Title: Structure of RRM3 Domain of Mip6 at 1.25 A Resolution Authors: Mohamad, N. / Bravo, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5d77S S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 9110.442 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: MIP6, YHR015W / Production host: ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / | ![]() #4: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.87 % |
---|---|
Crystal grow![]() | Temperature: 294 K / Method: vapor diffusion / pH: 8.5 Details: 0.2 M Lithium Sulfate; 0.1 M tris pH 8.5; 40% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→47.02 Å / Num. obs: 14132 / % possible obs: 74.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.31 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.25→1.27 Å |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5d77 Resolution: 1.251→28.758 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 23.39 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.251→28.758 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|