+Open data
-Basic information
Entry | Database: PDB / ID: 2du8 | ||||||
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Title | Crystal structure of human D-amino acid oxidase | ||||||
Components | D-amino-acid oxidase | ||||||
Keywords | OXIDOREDUCTASE / STRUCTURALLY AMBIVALENT PEPTIDES / CONFORMATIONAL VARIABILITY | ||||||
Function / homology | Function and homology information D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone ...D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / D-serine metabolic process / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / Glyoxylate metabolism and glycine degradation / dopamine biosynthetic process / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / Peroxisomal protein import / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kawazoe, T. / Tsuge, H. / Fukui, K. | ||||||
Citation | Journal: Protein Sci. / Year: 2006 Title: Crystal structure of human D-amino acid oxidase: Context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring Authors: Kawazoe, T. / Tsuge, H. / Pilone, M.S. / Fukui, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2du8.cif.gz | 292.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2du8.ent.gz | 234.7 KB | Display | PDB format |
PDBx/mmJSON format | 2du8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2du8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2du8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 2du8_validation.xml.gz | 55 KB | Display | |
Data in CIF | 2du8_validation.cif.gz | 73.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/2du8 ftp://data.pdbj.org/pub/pdb/validation_reports/du/2du8 | HTTPS FTP |
-Related structure data
Related structure data | 1an9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | There are 2 biological units in the asymmetric unit. The biological unit 1 consists of chain(s) A, B. The biological unit 2 consists of chain(s) G, J. |
-Components
#1: Protein | Mass: 39520.910 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET11B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14920, D-amino-acid oxidase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-BEZ / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.91 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 4000, 0.2M ammonium acetate, 0.1M sodium citrate, 12% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 24, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→116.25 Å / Num. obs: 49644 / % possible obs: 99.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.377 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AN9 Resolution: 2.5→46.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.63 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 1.696 / ESU R Free: 0.34 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.856 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→46.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 Å / Total num. of bins used: 20
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