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Yorodumi- PDB-2e4a: Crystal Structure of Human D-Amino Acid Oxidase in complex with o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e4a | |||||||||
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Title | Crystal Structure of Human D-Amino Acid Oxidase in complex with o-aminobenzoate | |||||||||
Components | D-amino-acid oxidaseD-amino acid oxidase | |||||||||
Keywords | OXIDOREDUCTASE / Structurally ambivalent peptide / O-Aminobenzoate complex | |||||||||
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-amino acid catabolic process / D-serine 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-amino acid catabolic process / D-serine 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Kawazoe, T. / Tsuge, H. / Imagawa, T. / Fukui, K. | |||||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2007 Title: Structural basis of d-DOPA oxidation by d-amino acid oxidase: Alternative pathway for dopamine biosynthesis. Authors: Kawazoe, T. / Tsuge, H. / Imagawa, T. / Aki, K. / Kuramitsu, 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 | 2e4a.cif.gz | 286.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e4a.ent.gz | 230.4 KB | Display | PDB format |
PDBx/mmJSON format | 2e4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/2e4a ftp://data.pdbj.org/pub/pdb/validation_reports/e4/2e4a | HTTPS FTP |
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-Related structure data
Related structure data | 2e48C 2e49C 2e82C 2du8S S: Starting model for refinement C: citing same article (ref.) |
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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) C, D. |
-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-BE2 / #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: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG 4000, 0.1M sodium citrate, 0.2M ammonium acetate, 10% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 27, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 45267 / % possible obs: 98.8 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.331 / % possible all: 98.2 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2DU8 Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.282 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R Free: 0.332 / 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: 39.917 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.597→2.665 Å / Total num. of bins used: 20
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