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Yorodumi- PDB-4gap: Structure of the Ndi1 protein from Saccharomyces cerevisiae in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gap | ||||||
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Title | Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with NAD+ | ||||||
Components | Rotenone-insensitive NADH-ubiquinone oxidoreductase | ||||||
Keywords | OXIDOREDUCTASE / Nucleotide-binding domains / Membrane | ||||||
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: 2.9 Å | ||||||
Authors | Iwata, M. / Lee, Y. / Yamashita, T. / Yagi, T. / Iwata, S. / Cameron, A.D. / Maher, M.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates. Authors: Iwata, M. / Lee, Y. / Yamashita, T. / Yagi, T. / Iwata, S. / Cameron, A.D. / Maher, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gap.cif.gz | 381.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gap.ent.gz | 314.9 KB | Display | PDB format |
PDBx/mmJSON format | 4gap.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/4gap ftp://data.pdbj.org/pub/pdb/validation_reports/ga/4gap | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 43 - 513 / Label seq-ID: 1 - 471
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-Components
#1: Protein | Mass: 52800.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's 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 | |
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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: 3.17 Å3/Da / Density % sol: 61.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM MES, 34% PEG 400, 100 mM NaCl, 2% Ethylene Glycol, 5% glycerol, 5 mM NAD+, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→40 Å / Num. all: 29065 / Num. obs: 29065 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.84 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 36.933 / SU ML: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.435 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.51 Å2 / Biso mean: 63.134 Å2 / Biso min: 14.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→39.84 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 6274 / Type: TIGHT THERMAL / Rms dev position: 2.63 Å / Weight position: 0.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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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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