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- PDB-3t2y: Crystal structure of sulfide:quinone oxidoreductase His132Ala var... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3t2y | ||||||
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Title | Crystal structure of sulfide:quinone oxidoreductase His132Ala variant from Acidithiobacillus ferrooxidans with bound disulfide | ||||||
![]() | Sulfide-quinone reductase, putative | ||||||
![]() | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / His132Ala variant / integral monotopic membrane protein / complex with disulfide | ||||||
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 | ![]() | 169.2 KB | Display | ![]() |
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PDB format | ![]() | 141.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 916.7 KB | Display | ![]() |
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Full document | ![]() | 926.7 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sx6C ![]() 3sxiC ![]() 3sy4C ![]() 3syiC ![]() 3sz0C ![]() 3szcC ![]() 3szfC ![]() 3szwC ![]() 3t0kC ![]() 3t14C ![]() 3t2kC C: citing same article ( |
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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 / Sugars , 2 types, 2 molecules A![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#1: Protein | Mass: 47397.570 Da / Num. of mol.: 1 / Mutation: H132A 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, 72 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/S2H.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/H2S.gif)
![](data/chem/img/S2H.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / |
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#4: Chemical | ChemComp-H2S / |
#5: Chemical | ChemComp-S2H / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.18 % |
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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 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: 2.5→50.9 Å / Num. all: 19125 / Num. obs: 15185 / % possible obs: 79.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 51.4 Å2 / Rmerge(I) obs: 0.123 / Rsym value: 0.123 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.893 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2733 / Rsym value: 0.893 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: refinement / Resolution: 2.5001→49.122 Å / SU ML: 0.98 / σ(F): 1.35 / Phase error: 26.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.434 Å2 / ksol: 0.327 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5001→49.122 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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