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Yorodumi- PDB-6oib: Crystal structure of human Sulfide Quinone Oxidoreductase in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oib | |||||||||
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Title | Crystal structure of human Sulfide Quinone Oxidoreductase in complex with coenzyme Q | |||||||||
Components | Sulfide:quinone oxidoreductase, mitochondrial | |||||||||
Keywords | OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information eukaryotic sulfide quinone oxidoreductase / glutathione-dependent sulfide quinone oxidoreductase activity / sulfide oxidation, using sulfide:quinone oxidoreductase / Sulfide oxidation to sulfate / sulfide:quinone oxidoreductase activity / quinone binding / FAD binding / mitochondrial inner membrane / mitochondrion Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | |||||||||
Authors | Banerjee, R. / Cho, U.S. / Kim, H. / Moon, S. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Cell Chem Biol / Year: 2019 Title: A Catalytic Trisulfide in Human Sulfide Quinone Oxidoreductase Catalyzes Coenzyme A Persulfide Synthesis and Inhibits Butyrate Oxidation. Authors: Landry, A.P. / Moon, S. / Kim, H. / Yadav, P.K. / Guha, A. / Cho, U.S. / Banerjee, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oib.cif.gz | 333.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oib.ent.gz | 281.6 KB | Display | PDB format |
PDBx/mmJSON format | 6oib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oib_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6oib_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 6oib_validation.xml.gz | 32.4 KB | Display | |
Data in CIF | 6oib_validation.cif.gz | 44.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/6oib ftp://data.pdbj.org/pub/pdb/validation_reports/oi/6oib | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46973.863 Da / Num. of mol.: 2 / Fragment: residues 42-450 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SQOR, SQRDL, CGI-44 / Production host: Escherichia coli (E. coli) References: UniProt: Q9Y6N5, Oxidoreductases; Acting on a sulfur group of donors; With a quinone or similar compound as acceptor |
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-Non-polymers , 5 types, 200 molecules
#2: Chemical | ChemComp-GOL / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-H2S / #6: 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: 3.11 Å3/Da / Density % sol: 60.5 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium tartrate dibasic, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12713 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→51.46 Å / Num. obs: 73848 / % possible obs: 96.9 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.079 / Net I/σ(I): 6 |
Reflection shell | Resolution: 2.03→2.08 Å / Rmerge(I) obs: 1.664 / Num. unique obs: 4449 / Rpim(I) all: 0.798 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→41.37 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.03→41.37 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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