[English] 日本語
Yorodumi- PDB-6k6r: Crystal structure of Saccharomyces cerevisiae single domain sulfu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6k6r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Saccharomyces cerevisiae single domain sulfurtranferase RDL2 | ||||||
Components | Thiosulfate sulfurtransferase RDL2, mitochondrial | ||||||
Keywords | TRANSFERASE / thiosulfate:cyanide sulfurtransferase / Rhodanese / Saccharomyces cerevisiae | ||||||
Function / homology | Function and homology information thiosulfate sulfurtransferase / thiosulfate sulfurtransferase activity / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.471 Å | ||||||
Authors | Li, H.J. / Wang, Q.D. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: Antioxidants / Year: 2021 Title: Saccharomyces cerevisiaeRhodanese RDL2 Uses the ArgResidue of the Active-Site Loop for Thiosulfate Decomposition Authors: Wang, Q.D. / Li, H. / Xia, Y. / Xun, L. / Li, H.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6k6r.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6k6r.ent.gz | 45.6 KB | Display | PDB format |
PDBx/mmJSON format | 6k6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/6k6r ftp://data.pdbj.org/pub/pdb/validation_reports/k6/6k6r | HTTPS FTP |
---|
-Related structure data
Related structure data | 3d1pS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 16758.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RDL2, AIM42, FMP31, YOR286W Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q08742, thiosulfate sulfurtransferase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
---|---|
Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3.5M Ammonium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→50 Å / Num. obs: 11448 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.99 / Net I/σ(I): 24.69 |
Reflection shell | Resolution: 2.47→2.51 Å |
-Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3D1P Resolution: 2.471→27.595 Å / Cross valid method: FREE R-VALUE
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.471→27.595 Å
|