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- PDB-3t2z: Crystal structure of sulfide:quinone oxidoreductase from Acidithi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t2z | |||||||||
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Title | Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans | |||||||||
![]() | Sulfide-quinone reductase, putative | |||||||||
![]() | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / integral monotopic membrane protein / acidithiobacillus ferrooxidans | |||||||||
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. / Solomonson, M. / Weiner, J.H. / James, M.N. | |||||||||
![]() | ![]() Title: Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. Authors: Cherney, M.M. / Zhang, Y. / Solomonson, M. / Weiner, J.H. / James, M.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 197.7 KB | Display | ![]() |
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PDB format | ![]() | 155.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 42.7 KB | Display | |
Data in CIF | ![]() | 61.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kpkC ![]() 3t31C ![]() 3h27 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47765.957 Da / Num. of mol.: 2 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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-Non-polymers , 6 types, 644 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/BU2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/S3H.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BU2.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/S3H.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-H2S / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.74 Å3/Da / Density % sol: 74.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 30% PEG 600, 0.1 M bis-tris buffer, 0.1M (NH4)2SO4, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 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: 2.299→50 Å / Num. all: 82166 / Num. obs: 82166 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.299→2.38 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 2 / Rsym value: 0.986 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3H27 ![]() 3h27 Resolution: 2.2994→40.918 Å / SU ML: 0.84 / σ(F): 1.34 / Phase error: 22.59 / 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: 58.847 Å2 / ksol: 0.341 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2994→40.918 Å
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Refine LS restraints |
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LS refinement shell |
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