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Yorodumi- PDB-5yjx: Structure of the Ndi1 protein from Saccharomyces cerevisiae in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yjx | ||||||
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Title | Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol. | ||||||
Components | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / monotopic membrane protein / NUCLEOTIDE-BINDING DOMAIN | ||||||
Function / homology | Function and homology information NADH:quinone reductase (non-electrogenic) / NADH oxidation / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / positive regulation of apoptotic process / mitochondrion / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å | ||||||
Authors | Yamasita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Harada, S. / Kita, K. / Hirano, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2018 Title: Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors Authors: Yamashita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Miyoshi, H. / Harada, S. / Kita, K. / Hirano, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yjx.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yjx.ent.gz | 160.5 KB | Display | PDB format |
PDBx/mmJSON format | 5yjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yj/5yjx ftp://data.pdbj.org/pub/pdb/validation_reports/yj/5yjx | HTTPS FTP |
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-Related structure data
Related structure data | 5yjwC 5yjyC 4g9kS S: Starting model for refinement 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
#1: Protein | Mass: 54236.074 Da / Num. of mol.: 2 / Fragment: UNP residues 28-513 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: NDI1, YML120C, YM7056.06C / Production host: Escherichia coli (E. coli) References: UniProt: P32340, NADH:quinone reductase (non-electrogenic) #2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.88 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50mM Mes(pH 6.0), 34%(v/v) PEG 400, 100mM NaCl, 2%(v/v) ethylene glycol, 5%(v/v) glycerol PH range: 6.0-6.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 17, 2014 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 22984 / % possible obs: 98.1 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4G9K Resolution: 3.21→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.857 / SU B: 23.808 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.603 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.365 Å2
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Refinement step | Cycle: 1 / Resolution: 3.21→20 Å
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Refine LS restraints |
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