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Open data
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Basic information
Entry | Database: PDB / ID: 1jeh | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE | ||||||
![]() | DIHYDROLIPOAMIDE DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / 2-oxoglutarate dehydrogenase complex / pyruvate dehydrogenase complex | ||||||
Function / homology | ![]() 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 / oxoglutarate dehydrogenase (succinyl-transferring) activity ...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 / oxoglutarate dehydrogenase (succinyl-transferring) activity / dihydrolipoyl dehydrogenase / dihydrolipoyl dehydrogenase activity / : / valine catabolic process / isoleucine catabolic process / acetyl-CoA biosynthetic process from pyruvate / oxoglutarate dehydrogenase complex / L-leucine catabolic process / : / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Toyoda, T. / Suzuki, K. / Sekigushi, T. / Reed, J. / Takenaka, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 193.4 KB | Display | ![]() |
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PDB format | ![]() | 153.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 536.3 KB | Display | ![]() |
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Full document | ![]() | 551.4 KB | Display | |
Data in XML | ![]() | 21.5 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3grsS S: Starting model for refinement |
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Similar structure data |
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Links
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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) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |