[English] 日本語
![](img/lk-miru.gif)
- PDB-6fgj: Crystal structure of the small alarmone synthethase 2 from Staphy... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6fgj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the small alarmone synthethase 2 from Staphylococcus aureus | ||||||
![]() | GTP pyrophosphokinase | ||||||
![]() | TRANSFERASE / Stringent response / alarmone / RelP / SAS2 / MRSA | ||||||
Function / homology | ![]() GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase / kinase activity / phosphorylation / GTP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bange, G. / Steinchen, W. / Vogt, M. / Altegoer, F. | ||||||
![]() | ![]() Title: Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ. Authors: Steinchen, W. / Vogt, M.S. / Altegoer, F. / Giammarinaro, P.I. / Horvatek, P. / Wolz, C. / Bange, G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 177.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 142 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 454 KB | Display | |
Data in XML | ![]() | 16.3 KB | Display | |
Data in CIF | ![]() | 21.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fgkC ![]() 6fgxC ![]() 5decS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 28094.139 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: ywaC, AB454_12730, AB466_12625, AB478_12605, AB526_12980, AFO97_10970, AFP37_10975, EP54_00695, EQ90_03295, ERS072738_01254, ERS074020_00750, HMPREF3211_00175 Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 0.1 M Tris pH 8.5, 0.2 M lithium sulfate, 30% (w/v) PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→49.06 Å / Num. obs: 24257 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 1 / Rmerge(I) obs: 0.0364 / Net I/σ(I): 20.37 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.58 / Num. unique obs: 10417 / CC1/2: 0.85 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5DEC Resolution: 2.251→49.06 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.03
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.251→49.06 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|