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Yorodumi- PDB-3szf: Crystal structure of sulfide:quinone oxidoreductase H198A variant... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3szf | ||||||
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Title | Crystal structure of sulfide:quinone oxidoreductase H198A variant from Acidithiobacillus ferrooxidans in complex with bound trisulfide and decylubiquinone | ||||||
Components | Sulfide-quinone reductase, putativeSulfide:quinone reductase | ||||||
Keywords | OXIDOREDUCTASE / sulfide:quinone oxidoreductase / His198Ala variant / integral monotopic membrane protein / complex with tetrasulfide and ubiquinone | ||||||
Function / homology | Function and homology information bacterial sulfide:quinone reductase / sulfide:quinone oxidoreductase activity / quinone binding / nucleotide binding / membrane Similarity search - Function | ||||||
Biological species | Acidithiobacillus ferrooxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / refinement / Resolution: 2.0994 Å | ||||||
Authors | Cherney, M.M. / Zhang, Y. / James, M.N.G. / Weiner, J.H. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3szf.cif.gz | 178.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3szf.ent.gz | 147.9 KB | Display | PDB format |
PDBx/mmJSON format | 3szf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sz/3szf ftp://data.pdbj.org/pub/pdb/validation_reports/sz/3szf | HTTPS FTP |
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-Related structure data
Related structure data | 3sx6C 3sxiC 3sy4C 3syiC 3sz0C 3szcC 3szwC 3t0kC 3t14C 3t2kC 3t2yC C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 47698.891 Da / Num. of mol.: 1 / Fragment: Sulfide:quinone oxidoreductase / Mutation: H198A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidithiobacillus ferrooxidans (bacteria) Strain: ATCC 23270 / DSM 14882 / NCIB 8455 / Gene: AFE_1792 / Production host: Escherichia coli (E. coli) / References: UniProt: B7JBP8 |
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#3: Sugar | ChemComp-LMT / |
-Non-polymers , 6 types, 287 molecules
#2: Chemical | ChemComp-FAD / | ||||||
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#4: Chemical | ChemComp-DCQ / | ||||||
#5: Chemical | ChemComp-H2S / #6: Chemical | ChemComp-S3H / | #7: Chemical | ChemComp-SO4 / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.02 % |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2010 |
Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→50 Å / Num. all: 32310 / Num. obs: 30889 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 2.099→2.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.642 / % possible all: 73.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.7.1_743) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: refinement / Resolution: 2.0994→43.369 Å / SU ML: 0.66 / σ(F): 1.34 / Phase error: 22.55 / 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: 39.191 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.0994→43.369 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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