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Yorodumi- PDB-1c0k: CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c0k | |||||||||
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Title | CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE | |||||||||
Components | PROTEIN (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 / SYNCHROTRON / Resolution: 1.46 Å | |||||||||
Authors | Umhau, S. / Molla, G. / Diederichs, K. / Pilone, M.S. / Ghisla, S. / Welte, W. / Pollegioni, L. | |||||||||
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 | 1c0k.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c0k.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 1c0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c0k_validation.pdf.gz | 691.2 KB | Display | wwPDB validaton report |
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Full document | 1c0k_full_validation.pdf.gz | 697.2 KB | Display | |
Data in XML | 1c0k_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 1c0k_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c0/1c0k ftp://data.pdbj.org/pub/pdb/validation_reports/c0/1c0k | 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
#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, D-amino-acid oxidase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-LAC / |
#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: 3.13 Å3/Da / Density % sol: 60.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8345 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→100 Å / Num. obs: 515122 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.1 |
Reflection | *PLUS Highest resolution: 1.46 Å / Lowest resolution: 100 Å / Num. obs: 83893 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Num. measured all: 515122 |
Reflection shell | *PLUS % possible obs: 91.2 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Resolution: 1.46→100 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.46→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): 0 / Rfactor obs: 0.112 / Rfactor Rfree: 0.161 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 1.73 |