[English] 日本語
Yorodumi- PDB-1evi: THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1evi | ||||||
---|---|---|---|---|---|---|---|
Title | THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE | ||||||
Components | D-AMINO ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME | ||||||
Function / homology | Function and homology information Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / presynaptic active zone ...Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / peroxisome / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Mizutani, H. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Miura, R. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2000 Title: Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin. Authors: Mizutani, H. / Miyahara, I. / Hirotsu, K. / Nishina, Y. / Shiga, K. / Setoyama, C. / Miura, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1evi.cif.gz | 154.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1evi.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 1evi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1evi_validation.pdf.gz | 559.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1evi_full_validation.pdf.gz | 582.7 KB | Display | |
Data in XML | 1evi_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | 1evi_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/1evi ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1evi | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 38612.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Organ: KIDNEY / Plasmid: PET11D / Production host: Escherichia coli (E. coli) / References: UniProt: P00371, D-amino-acid oxidase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % | |||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.3 Details: PEG 4000, sodium acetate, sodium citrate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Details: Setoyama, C., (1996) J. Biochem., 1114. | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.708 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 4, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.708 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 23734 / % possible obs: 96.5 % / Observed criterion σ(I): 1 / Redundancy: 3.56 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.151 / Num. unique all: 2338 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 86285 |
Reflection shell | *PLUS % possible obs: 95.9 % |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→10 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|