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Yorodumi- PDB-1dao: COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-ME... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dao | ||||||
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Title | COVALENT ADDUCT OF D-AMINO ACID OXIDASE FROM PIG KIDNEY WITH 3-METHYL-2-OXO-VALERIC ACID | ||||||
Components | D-AMINO ACID OXIDASE | ||||||
Keywords | FLAVOENZYME / FAD COFACTOR / OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / peroxisomal matrix ...Glyoxylate metabolism and glycine degradation / Peroxisomal protein import / D-alanine catabolic process / D-amino-acid oxidase / D-amino-acid oxidase activity / proline catabolic process / D-serine catabolic process / D-amino acid catabolic process / dopamine biosynthetic process / peroxisomal matrix / digestion / FAD binding / peroxisome / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / DENSITY AVERAGING / Resolution: 3.2 Å | ||||||
Authors | Todone, F. / Mattevi, A. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: Active site plasticity in D-amino acid oxidase: a crystallographic analysis. Authors: Todone, F. / Vanoni, M.A. / Mozzarelli, A. / Bolognesi, M. / Coda, A. / Curti, B. / Mattevi, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dao.cif.gz | 543.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dao.ent.gz | 449.5 KB | Display | PDB format |
PDBx/mmJSON format | 1dao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/1dao ftp://data.pdbj.org/pub/pdb/validation_reports/da/1dao | HTTPS FTP |
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-Related structure data
Related structure data | 1ddoC 1kifS 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 39377.812 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: KIDNEY / Organelle: PEROXISOME / References: UniProt: P00371, D-amino-acid oxidase #2: Chemical | ChemComp-FAB / #3: 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: 3.48 Å3/Da / Density % sol: 60 % |
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Crystal grow | pH: 8.3 Details: PROTEIN WAS CRYSTALLIZED FROM 0.5 M AMMONIUM SUCCINATE, 100 MM TRIS PH 8.3, 2 MM BENZOATE THEN SOAKED IN 20 MM 3-METHYL-2-OXO-BUTYRIC ACID |
Crystal grow | *PLUS Method: vapor diffusion, hanging drop |
Components of the solutions | *PLUS Conc.: 0.6 M / Common name: ammonium succinate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→20 Å / Num. obs: 72287 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 5 |
Reflection shell | Resolution: 3.2→3.25 Å / Redundancy: 4 % / Rmerge(I) obs: 0.352 / Mean I/σ(I) obs: 2 / % possible all: 99.1 |
Reflection | *PLUS Num. measured all: 433795 |
Reflection shell | *PLUS % possible obs: 99.1 % |
-Processing
Software |
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Refinement | Method to determine structure: DENSITY AVERAGING Starting model: PDB ENTRY 1KIF Resolution: 3.2→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT Details: THE 8 SUBUNITS WERE KEPT IDENTICAL EXCEPT FOR RESIDUES 56 - 65, 125 - 130, 157 - 180, 254, 265, 270, 288, THAT WERE RESTRAINED.
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Solvent computation | Solvent model: BABINET | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_plane_restr / Dev ideal: 0.016 |