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- PDB-3syi: Crystal structure of sulfide:quinone oxidoreductase Ser126Ala var... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3syi | ||||||
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Title | Crystal structure of sulfide:quinone oxidoreductase Ser126Ala variant from Acidithiobacillus ferrooxidans using 7.0 keV diffraction data | ||||||
![]() | Sulfide-quinone reductase, putative | ||||||
![]() | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / Ser126Ala 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.4 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3sx6C ![]() 3sxiC ![]() 3sy4C ![]() 3sz0C ![]() 3szcC ![]() 3szfC ![]() 3szwC ![]() 3t0kC ![]() 3t14C ![]() 3t2kC ![]() 3t2yC ![]() 3kpg C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 47749.957 Da / Num. of mol.: 1 / Mutation: S126A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: ![]() ![]() |
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#3: Sugar | ChemComp-LMT / |
-Non-polymers , 4 types, 111 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / | ||||
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#4: Chemical | ChemComp-H2S / #5: Chemical | ChemComp-SO4 / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.72 % |
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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, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2010 |
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49 Å / Num. obs: 48437 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.3 / Rsym value: 0.833 / % possible all: 69.2 |
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Processing
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Refinement | Method to determine structure: refinement Starting model: PDB ENTRY 3KPG ![]() 3kpg Resolution: 2.2001→42.069 Å / SU ML: 0.7 / σ(F): 1.34 / Phase error: 27.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.876 Å2 / ksol: 0.332 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2001→42.069 Å
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Refine LS restraints |
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LS refinement shell |
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