[English] 日本語
![](img/lk-miru.gif)
- PDB-3sxi: Crystal structure of sulfide:quinone oxidoreductase Cys128Ala var... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3sxi | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone | ||||||
![]() | Sulfide-quinone reductase, putative | ||||||
![]() | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / Cys128Ala variant / integral monotopic membrane protein / complex with sulfide | ||||||
Function / homology | ![]() bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cherney, M.M. / Zhang, Y. / James, M.N.G. / Weiner, J.H. | ||||||
![]() | ![]() Title: Structure-activity characterization of sulfide:quinone oxidoreductase variants. Authors: Cherney, M.M. / Zhang, Y. / James, M.N. / Weiner, J.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 178.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 148.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 21.6 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sx6C ![]() 3sy4C ![]() 3syiC ![]() 3sz0C ![]() 3szcC ![]() 3szfC ![]() 3szwC ![]() 3t0kC ![]() 3t14C ![]() 3t2kC ![]() 3t2yC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 47733.895 Da / Num. of mol.: 1 / Mutation: C128A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: ![]() ![]() |
---|---|
#3: Sugar | ChemComp-LMT / |
-Non-polymers , 5 types, 282 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/DCQ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCQ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||
---|---|---|---|
#4: Chemical | ChemComp-DCQ / | ||
#5: Chemical | ChemComp-SO4 / | ||
#6: Chemical | ChemComp-H2S / #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% PEG 600, 0.1 M bis-tris buffer,0.1 M MgSO4, 0.05% DDM, 2mM decylubiquinone, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 28, 2009 |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.1792→50 Å / Num. all: 28719 / Num. obs: 28461 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 33.44 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 2.1792→2.26 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.889 / Mean I/σ(I) obs: 2.04 / Num. unique all: 2815 / Rsym value: 0.889 / % possible all: 97.7 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.769 Å2 / ksol: 0.347 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1792→49.128 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|