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- PDB-5yjx: Structure of the Ndi1 protein from Saccharomyces cerevisiae in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5yjx | ||||||
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Title | Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol. | ||||||
![]() | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | ||||||
![]() | OXIDOREDUCTASE / monotopic membrane protein / NUCLEOTIDE-BINDING DOMAIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yamasita, T. / Inaoka, D.K. / Shiba, T. / Oohashi, T. / Iwata, S. / Yagi, T. / Kosaka, H. / Harada, S. / Kita, K. / Hirano, K. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.7 KB | Display | ![]() |
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PDB format | ![]() | 160.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 37.6 KB | Display | |
Data in CIF | ![]() | 49.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yjwC ![]() 5yjyC ![]() 4g9kS S: Starting model for refinement 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
#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.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: NDI1, YML120C, YM7056.06C / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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