+Open data
-Basic information
Entry | Database: PDB / ID: 1jeh | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE | ||||||
Components | DIHYDROLIPOAMIDE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / 2-oxoglutarate dehydrogenase complex / pyruvate dehydrogenase complex | ||||||
Function / homology | Function and homology information : / Glyoxylate metabolism and glycine degradation / Glycine degradation / Pyruvate metabolism / Lysine catabolism / pyruvate dehydrogenase activity / Citric acid cycle (TCA cycle) / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / glycine cleavage complex ...: / Glyoxylate metabolism and glycine degradation / Glycine degradation / Pyruvate metabolism / Lysine catabolism / pyruvate dehydrogenase activity / Citric acid cycle (TCA cycle) / glycine dehydrogenase (decarboxylating) activity / glycine catabolic process / glycine cleavage complex / L-leucine catabolic process / oxoglutarate dehydrogenase (succinyl-transferring) activity / oxoglutarate dehydrogenase complex / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / valine catabolic process / isoleucine catabolic process / : / acetyl-CoA biosynthetic process from pyruvate / : / L-serine biosynthetic process / 2-oxoglutarate metabolic process / pyruvate metabolic process / hydrogen peroxide metabolic process / mitochondrial nucleoid / flavin adenine dinucleotide binding / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Toyoda, T. / Suzuki, K. / Sekigushi, T. / Reed, J. / Takenaka, A. | ||||||
Citation | Journal: J.Biochem. / Year: 1998 Title: Crystal structure of eucaryotic E3, lipoamide dehydrogenase from yeast. Authors: Toyoda, T. / Suzuki, K. / Sekiguchi, T. / Reed, L.J. / Takenaka, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jeh.cif.gz | 193.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jeh.ent.gz | 153.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jeh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/1jeh ftp://data.pdbj.org/pub/pdb/validation_reports/je/1jeh | HTTPS FTP |
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-Related structure data
Related structure data | 3grsS S: Starting model for refinement |
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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: 51623.992 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P09624, dihydrolipoyl dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.5 Å3/Da / Density % sol: 50.8 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: microdialysis / pH: 7 / Details: PEG6000, pH 7.00, MICRODIALYSIS, temperature 298K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: Toyoda, T., (1997) J.Biochem.(Tokyo), 121, 1. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 / Wavelength: 1 Å |
Detector | Type: FUJI / Detector: IMAGE PLATE |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→100 Å / Num. obs: 33372 / % possible obs: 80.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Rmerge(I) obs: 0.067 |
Reflection shell | Resolution: 2.4→2.68 Å / % possible all: 42.7 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 100 Å / Redundancy: 2.9 % / Num. measured all: 97677 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3GRS Resolution: 2.4→10 Å / σ(F): 4
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Displacement parameters | Biso mean: 35.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.51 Å / Total num. of bins used: 8 /
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 10 % / Rfactor Rfree: 0.26 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 35.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_improper_angle_d / Dev ideal: 0.763 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.303 / % reflection Rfree: 10 % / Rfactor Rwork: 0.286 |