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- PDB-1ivh: STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ivh | ||||||
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Title | STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS RESOLUTION: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY | ||||||
![]() | ISOVALERYL-COA DEHYDROGENASE | ||||||
![]() | OXIDOREDUCTASE / ACYL-COA DEHYDROGENASE / FLAVOPROTEIN / ISOVALERYL-COA / ISOVALERIC ACIDEMIA | ||||||
Function / homology | ![]() isovaleryl-CoA dehydrogenase / short-chain acyl-CoA dehydrogenase / : / 3-methylbutanoyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix ...isovaleryl-CoA dehydrogenase / short-chain acyl-CoA dehydrogenase / : / 3-methylbutanoyl-CoA dehydrogenase activity / fatty acid beta-oxidation using acyl-CoA dehydrogenase / L-leucine catabolic process / branched-chain amino acid catabolic process / Branched-chain amino acid catabolism / flavin adenine dinucleotide binding / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tiffany, K.A. / Roberts, D.L. / Wang, M. / Paschke, R. / Mohsen, A.-W.A. / Vockley, J. / Kim, J.J.P. | ||||||
![]() | ![]() Title: Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity,. Authors: Tiffany, K.A. / Roberts, D.L. / Wang, M. / Paschke, R. / Mohsen, A.W. / Vockley, J. / Kim, J.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 308.2 KB | Display | ![]() |
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PDB format | ![]() | 252.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 866.3 KB | Display | ![]() |
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Full document | ![]() | 912.1 KB | Display | |
Data in XML | ![]() | 37.4 KB | Display | |
Data in CIF | ![]() | 54.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1mdeS 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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Unit cell |
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Components
#1: Protein | Mass: 43120.477 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: EACH SUBUNIT CONTAINS ONE NON-COVALENTLY BOUND FAD MOLECULE AND ONE NON-COVALENTLY BOUND COA PER SULFIDE MOLECULE Source: (gene. exp.) ![]() Description: THE CDNA WAS ALTERED TO ACCOMMODATE ESCHERICHIA COLI CODON USAGE IN ORDER TO ACHIEVE A HIGH LEVEL OF EXPRESSION. THE MOLECULE WAS THEN CLONED, EXPRESSED, AND PURIFIED AS DESCRIBED IN\: ...Description: THE CDNA WAS ALTERED TO ACCOMMODATE ESCHERICHIA COLI CODON USAGE IN ORDER TO ACHIEVE A HIGH LEVEL OF EXPRESSION. THE MOLECULE WAS THEN CLONED, EXPRESSED, AND PURIFIED AS DESCRIBED IN\: MOHSEN, A.W. AND VOCKLEY, J. (1995) BIOCHEMISTRY, 34\:10146-10152 Gene: IVD / Organ: LIVER / Organelle: MITOCHONDRIA / Plasmid: PKMHIVD / Cellular location (production host): CYTOPLASM / Production host: ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-COS / #4: Water | ChemComp-HOH / | Compound details | COA PERSULFIDE | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 51 % / Description: A HOMOTETRAMER WAS USED AS THE SEARCH MODEL | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / pH: 8.5 Details: PROTEIN WAS CRYSTALLIZED FROM 8% PEG 8000, 0.1 M TRIS, PH 8.5 AT 19 DEGREES CELSIUS., temperature 292K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 42529 / % possible obs: 82.2 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.219 / % possible all: 61 |
Reflection shell | *PLUS % possible obs: 61 % / Rmerge(I) obs: 0.219 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1MDE Resolution: 2.6→10 Å / Rfactor Rfree error: 0.002 / Cross valid method: FREE R / σ(F): 1
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Displacement parameters | Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.283 |