[English] 日本語
Yorodumi- PDB-1ivh: STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ivh | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF HUMAN ISOVALERYL-COA DEHYDROGENASE AT 2.6 ANGSTROMS RESOLUTION: STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY | ||||||
Components | ISOVALERYL-COA DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / ACYL-COA DEHYDROGENASE / FLAVOPROTEIN / ISOVALERYL-COA / ISOVALERIC ACIDEMIA | ||||||
Function / homology | Function and homology information isovaleryl-CoA dehydrogenase / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / : / 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 / 3-methylbutanoyl-CoA dehydrogenase activity / short-chain acyl-CoA dehydrogenase / : / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tiffany, K.A. / Roberts, D.L. / Wang, M. / Paschke, R. / Mohsen, A.-W.A. / Vockley, J. / Kim, J.J.P. | ||||||
Citation | Journal: Biochemistry / Year: 1997 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ivh.cif.gz | 308.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ivh.ent.gz | 252.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ivh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ivh_validation.pdf.gz | 866.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ivh_full_validation.pdf.gz | 912.1 KB | Display | |
Data in XML | 1ivh_validation.xml.gz | 37.4 KB | Display | |
Data in CIF | 1ivh_validation.cif.gz | 54.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/1ivh ftp://data.pdbj.org/pub/pdb/validation_reports/iv/1ivh | HTTPS FTP |
-Related structure data
Related structure data | 1mdeS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) 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: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P26440, isovaleryl-CoA dehydrogenase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-COS / #4: Water | ChemComp-HOH / | Compound details | COA PERSULFIDE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 51 % / Description: A HOMOTETRAMER WAS USED AS THE SEARCH MODEL | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 277 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MDE Resolution: 2.6→10 Å / Rfactor Rfree error: 0.002 / Cross valid method: FREE R / σ(F): 1
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.72 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.283 |