[English] 日本語
![](img/lk-miru.gif)
- PDB-8gkv: Crystal structure of anti-adaptor IraP that regulates RpoS proteolysis -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8gkv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of anti-adaptor IraP that regulates RpoS proteolysis | ||||||
![]() | Anti-adapter protein IraP | ||||||
![]() | GENE REGULATION / alpha helix | ||||||
Function / homology | Sigma-S stabilisation anti-adaptor protein / Sigma-S stabilisation anti-adaptor protein / anti-sigma factor antagonist activity / cellular response to phosphate starvation / negative regulation of protein catabolic process / cytoplasm / Anti-adapter protein IraP![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Leucine zipper-like protein | ||||||
![]() | Shaw, G.X. / Gan, J. / Suburaman, P. / Battesti, A. / Zhou, Y.N. / Wickner, S. / Gottesman, S. / Ji, X. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural and functional study of anti-adaptor IraP-mediated regulation of RpoS proteolysis Authors: Tripathi, A. / Hoskins, J. / Shaw, G.X. / Gan, J. / Tong, S. / Battesti, A. / Jenkins, L.M. / Ji, X. / Wickner, S. / Gottesman, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 49.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 33.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10048.501 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-86 / Mutation: C23S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 43 molecules ![](data/chem/img/EPE.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EPE / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-TRS / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.65 % / Mosaicity: 0.806 ° |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: Tri-Na citrate, MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin | Operator: k+l,h+l,-l / Fraction: 0.17 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.35→30 Å / Num. obs: 6391 / % possible obs: 95.4 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.051 / Χ2: 1.093 / Net I/σ(I): 16 / Num. measured all: 21575 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: ![]() |
---|
-
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 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.6 Å2 / Biso mean: 55.296 Å2 / Biso min: 21.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.351→29.064 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
|