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- PDB-4yjf: Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylami... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yjf | ||||||
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Title | Crystal structure of DAAO(Y228L/R283G) variant (S-methylbenzylamine binding form) | ||||||
![]() | (D-amino-acid ...) x 2 | ||||||
![]() | OXIDOREDUCTASE / amine oxidase / Variant of D-amino acid oxidase / S-methylbenzylamine binding form | ||||||
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 / digestion ...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 / digestion / presynaptic active zone / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / FAD binding / cell projection / peroxisome / extracellular region / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Nakano, S. / Yasukawa, K. / Kawahara, N. / Ishitsubo, E. / Tokiwa, H. / Asano, Y. | ||||||
![]() | ![]() Title: Crystal structure of DAAO variant Authors: Nakano, S. / Yasukawa, K. / Kawahara, N. / Ishitsubo, E. / Tokiwa, H. / 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 | ![]() | 152.9 KB | Display | ![]() |
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PDB format | ![]() | 118.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4yjdC ![]() 4yjgC ![]() 4yjhC ![]() 3wgtS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 1 - 338 / Label seq-ID: 1 - 338
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Components
-D-amino-acid ... , 2 types, 2 molecules AB
#1: Protein | Mass: 38563.848 Da / Num. of mol.: 1 / Fragment: UNP residues 1-341 / Mutation: Y228L, R283G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 38349.590 Da / Num. of mol.: 1 / Fragment: UNP residues 1-339 / Mutation: Y228L, R283G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 62 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/98B.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/98B.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 30% PEG4000, 0.1M Tris-HCl(pH 8.5), 0.2M Lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→23.6 Å / Num. obs: 34607 / % possible obs: 95 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 46.7 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 7.2 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3WGT Resolution: 2.2→23.6 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.797 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.213 / 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: 33.115 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→23.6 Å
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Refine LS restraints |
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