+Open data
-Basic information
Entry | Database: PDB / ID: 1ivi | ||||||
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Title | Crystal Structure of pig dihydrolipoamide dehydrogenase | ||||||
Components | dihydrolipoamide dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / 2-OXOGLUTARATE DEHYDROGENASE COMPLEX / PYRUVATE DEHYDROGENASE COMPLEX | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 8 Å | ||||||
Authors | Toyoda, T. / Kobayashi, R. / Sekiguchi, T. / Koike, K. / Koike, M. / Takenaka, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary X-ray analysis of pig E3, lipoamide dehydrogenase. Authors: Toyoda, T. / Kobayashi, R. / Sekiguchi, T. / Koike, K. / Koike, M. / Takenaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ivi.cif.gz | 74.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ivi.ent.gz | 52.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ivi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivi ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivi | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 40698.164 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: dihydrolipoyl dehydrogenase |
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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: 6.43 Å3/Da / Density % sol: 80.88 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1.04 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 8→50 Å / Num. all: 13615 / Num. obs: 5838 / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Highest resolution: 8 Å / % possible obs: 98 % / Num. measured all: 13615 |
-Processing
Software |
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Refinement | Resolution: 8→50 Å / Rfactor Rwork: 0.378 Details: The coordinates for only the alpha carbons are present in the structure. | |||||||||||||||
Refinement step | Cycle: LAST / Resolution: 8→50 Å
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Refinement | *PLUS Lowest resolution: 50 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.379 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS |