[English] 日本語
![](img/lk-miru.gif)
- PDB-8tfs: Crystal structure of the Rhodanese-like domain of Vretifemale_108... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8tfs | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Rhodanese-like domain of Vretifemale_1082 from Volvox reticuliferus | ||||||
![]() | Rhodanese domain-containing protein | ||||||
![]() | TRANSFERASE / Rhodanese / sulfur transferase | ||||||
Function / homology | Calcium sensing receptor, plant / de-etiolation / regulation of stomatal closure / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / cellular response to calcium ion / Rhodanese domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arbing, M.A. / Jonikas, M. / Yeates, T.O. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystal structure of the Rhodanese-like domain of Vretifemale_1082 from Volvox reticuliferus Authors: Arbing, M.A. / Jonikas, M. / Yeates, T.O. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 206.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 138.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 417.7 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 20025.602 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.23 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 10% PEG3350. Cryoprotectant: 0.2 M L-Proline, 0.1 M HEPES pH 7.5, 23% PEG3350, 5% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72932 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→57.5 Å / Num. obs: 50761 / % possible obs: 99.88 % / Redundancy: 9.8 % / Biso Wilson estimate: 40.04 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.08409 / Rpim(I) all: 0.02846 / Rrim(I) all: 0.08888 / Net I/σ(I): 14.03 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.8456 / Mean I/σ(I) obs: 1.77 / Num. unique obs: 2645 / CC1/2: 0.9 / CC star: 0.973 / Rpim(I) all: 0.2763 / Rrim(I) all: 0.8902 / % possible all: 99.77 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→53.26 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -12.8609050956 Å / Origin y: -1.60037038005 Å / Origin z: 12.8250411556 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |