[English] 日本語
Yorodumi- PDB-1is2: Crystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver -
+Open data
-Basic information
Entry | Database: PDB / ID: 1is2 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Peroxisomal Acyl-CoA Oxidase-II from Rat Liver | ||||||
Components | acyl-CoA oxidase | ||||||
Keywords | OXIDOREDUCTASE / FAD | ||||||
Function / homology | Function and homology information very long-chain fatty acid beta-oxidation / alpha-linolenic acid (ALA) metabolism / palmitoyl-CoA oxidase activity / acyl-CoA oxidase / Beta-oxidation of very long chain fatty acids / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / Peroxisomal protein import / very long-chain fatty acid metabolic process / fatty acid catabolic process ...very long-chain fatty acid beta-oxidation / alpha-linolenic acid (ALA) metabolism / palmitoyl-CoA oxidase activity / acyl-CoA oxidase / Beta-oxidation of very long chain fatty acids / acyl-CoA oxidase activity / fatty acid beta-oxidation using acyl-CoA oxidase / Peroxisomal protein import / very long-chain fatty acid metabolic process / fatty acid catabolic process / hydrogen peroxide biosynthetic process / peroxisomal membrane / prostaglandin metabolic process / lipid homeostasis / fatty acid oxidation / peroxisomal matrix / FAD binding / generation of precursor metabolites and energy / fatty acid binding / PDZ domain binding / lipid metabolic process / peroxisome / flavin adenine dinucleotide binding / spermatogenesis / protein homodimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å | ||||||
Authors | Nakajima, Y. / Miyahara, I. / Hirotsu, K. | ||||||
Citation | Journal: J.Biochem. / Year: 2002 Title: Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase. Authors: Nakajima, Y. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Tamaoki, H. / Miura, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1is2.cif.gz | 264.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1is2.ent.gz | 211.9 KB | Display | PDB format |
PDBx/mmJSON format | 1is2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/1is2 ftp://data.pdbj.org/pub/pdb/validation_reports/is/1is2 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer in the asymmetric unit. |
-Components
#1: Protein | Mass: 74784.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET11d / Production host: Escherichia coli (E. coli) / References: UniProt: P07872, acyl-CoA oxidase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.92 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 20000, potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 69647 / Num. obs: 69647 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.2→2.27 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.1 / Num. unique all: 6152 / % possible all: 85.3 |
Reflection | *PLUS Highest resolution: 2.2 Å / Num. measured all: 344046 / Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 85.3 % / Num. unique obs: 6152 / Num. measured obs: 22267 / Rmerge(I) obs: 0.283 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MIRAS / Resolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: RANDOM
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.8 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.209 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.209 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|