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- PDB-5wwv: Crystal structure of porcine kidney D-amino acid oxidase mutant (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wwv | ||||||
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Title | Crystal structure of porcine kidney D-amino acid oxidase mutant (I230A/R283G) | ||||||
![]() | D-amino-acid oxidase | ||||||
![]() | OXIDOREDUCTASE / OXIDASE / FAD-BINDING | ||||||
Function / homology | ![]() Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / 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 / presynaptic active zone ...Peroxisomal protein import / Glyoxylate metabolism and glycine degradation / 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 / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / cell projection / peroxisome / extracellular region / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Motojima, F. / Yasukawa, K. / Ohno, A. / Asano, Y. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Tailoring D-amino acid oxidase from the pid kidney to R-stereoselective amine oxidase and its use in the deracemization of 4-chlorobenzhydrylamine Authors: Yasukawa, K. / Motojima, F. / Ohno, A. / Asano, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 557.8 KB | Display | ![]() |
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PDB format | ![]() | 461.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5wx2C ![]() 3wgtS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 39235.590 Da / Num. of mol.: 8 / Mutation: I230A, R283G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 85 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/7V3.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/7V3.gif)
![](data/chem/img/MPD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-7V3 / ( #4: Chemical | ChemComp-MPD / ( #5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.2 % / Description: Rod shaped |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 10% PEG 3350, 15% MPD, 200 mM Lithium sulfate, 100 mM Bis-Tris-HCl pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: CCD / Date: Nov 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→144.49 Å / Num. obs: 52954 / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.111 / Rsym value: 0.121 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 3.2→3.37 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 3.7 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WGT Resolution: 3.2→48.73 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.898 / SU B: 24.691 / SU ML: 0.412 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.526 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.419 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→48.73 Å
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Refine LS restraints |
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