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Yorodumi- PDB-1c0l: D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c0l | ||||||
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Title | D-AMINO ACID OXIDASE: STRUCTURE OF SUBSTRATE COMPLEXES AT VERY HIGH RESOLUTION REVEAL THE CHEMICAL REACTTION MECHANISM OF FLAVIN DEHYDROGENATION | ||||||
Components | D-AMINO ACID OXIDASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVIN CONTAINING PROTEIN ALPHA-BETA-ALPHA MOTIF | ||||||
Function / homology | Function and homology information 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 | Rhodosporidium toruloides (fungus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.73 Å | ||||||
Authors | Umhau, S. / Molla, G. / Diederichs, K. / Pilone, M.S. / Ghisla, S. / Welte, W. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: The x-ray structure of D-amino acid oxidase at very high resolution identifies the chemical mechanism of flavin-dependent substrate dehydrogenation. Authors: Umhau, S. / Pollegioni, L. / Molla, G. / Diederichs, K. / Welte, W. / Pilone, M.S. / Ghisla, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c0l.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c0l.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 1c0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c0l_validation.pdf.gz | 708.5 KB | Display | wwPDB validaton report |
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Full document | 1c0l_full_validation.pdf.gz | 716.5 KB | Display | |
Data in XML | 1c0l_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 1c0l_validation.cif.gz | 35.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/1c0l ftp://data.pdbj.org/pub/pdb/validation_reports/c0/1c0l | HTTPS FTP |
-Related structure data
-Links
-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.) Rhodosporidium toruloides (fungus) / Plasmid: PT7.7 / Production host: Escherichia coli (E. coli) / References: UniProt: P80324 |
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#2: Chemical | ChemComp-FLA / |
#3: Chemical | ChemComp-FAD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 60.58 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100MM HEPES 16% POLYETHYLENE GLYCOL PEG 200MM AMMONIUM SULFATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 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: 1.7→100 Å / Num. all: 230642 / Num. obs: 52652 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.117 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 1.73→1.79 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.282 / % possible all: 93.8 |
Reflection | *PLUS Num. measured all: 230642 / Rmerge(I) obs: 0.11 |
Reflection shell | *PLUS % possible obs: 96.7 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 2.3 |
-Processing
Software |
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Refinement | Resolution: 1.73→100 Å / σ(F): 4 / σ(I): 4 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.73→100 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 100 Å / σ(F): 4 / Rfactor Rwork: 0.162 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 2.48 |