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- PDB-1c0i: CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1c0i | |||||||||
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Title | CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANTHRANYLATE MOLECULES | |||||||||
![]() | D-AMINO ACID OXIDASE | |||||||||
![]() | OXIDOREDUCTASE / FLAVIN CONTAINING PROTEIN / ALPHA-BETA-ALPHA MOTIF | |||||||||
Function / homology | ![]() D-glutamate oxidase activity / D-aspartate oxidase activity / D-amino acid metabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / nitrogen utilization / D-amino acid catabolic process / aspartate catabolic process / peroxisomal matrix / FAD binding / peroxisome Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Pollegioni, L. / Diederichs, K. / Molla, G. / Umhau, S. / Welte, W. / Ghisla, S. / Pilone, M.S. | |||||||||
![]() | ![]() Title: Yeast d-amino Acid oxidase: structural basis of its catalytic properties Authors: Pollegioni, L. / Diederichs, K. / Molla, G. / Umhau, S. / Welte, W. / Ghisla, S. / Pilone, M.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.2 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.9 KB | Display | ![]() |
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Full document | ![]() | 468.3 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 39614.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.94 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100MM HEPES, POLYETHYLENE GLYCOL 10000, 200MM AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃Details: Umhau, S., (2000) Proc.Natl.Acad.Sci.U.S.J., 97, 12463. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 75551 / Num. obs: 74424 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.287 / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 100 Å / Num. obs: 75551 / Num. measured all: 193503 |
Reflection shell | *PLUS Lowest resolution: 2 Å / % possible obs: 99.8 % / Mean I/σ(I) obs: 1.9 |
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Processing
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Refinement | Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 4 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 50 Å / σ(F): 4 / Rfactor obs: 0.205 / Rfactor Rfree: 0.248 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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