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Open data
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Basic information
Entry | Database: PDB / ID: 6a0y | ||||||
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Title | Mandelate oxidase mutant-Y128F with Benzoic acid | ||||||
![]() | 4-hydroxymandelate oxidase | ||||||
![]() | FLAVOPROTEIN / FMN-dependent oxidase | ||||||
Function / homology | ![]() 4-hydroxymandelate oxidase / oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor / vancomycin biosynthetic process / : / fatty acid alpha-oxidation / L-lactate dehydrogenase activity / FMN binding / peroxisome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T.L. / Lin, K.H. | ||||||
![]() | ![]() Title: Biochemical and structural explorations of alpha-hydroxyacid oxidases reveal a four-electron oxidative decarboxylation reaction. Authors: Yeh, H.W. / Lin, K.H. / Lyu, S.Y. / Li, Y.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Hsu, N.S. / Wu, C.J. / Li, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 93.3 KB | Display | ![]() |
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PDB format | ![]() | 68.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zzqC ![]() 5zzsC ![]() 5zzxC ![]() 5zzyC ![]() 6a00C ![]() 6a0dC ![]() 6a0gC ![]() 6a0mC ![]() 6a0oC ![]() 6a11C ![]() 6a1aC ![]() 3sgzS 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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Unit cell |
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Components
#1: Protein | Mass: 40029.562 Da / Num. of mol.: 1 / Mutation: Y128F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-FMN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 35% Tascimate, 0.1M Bis-Tris propane pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 64768 / % possible obs: 100 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.022 / Χ2: 0.957 / Net I/σ(I): 31 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6404 / CC1/2: 0.826 / Rpim(I) all: 0.28 / Χ2: 0.744 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SGZ Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.538 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / 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: 18.409 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→30 Å
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Refine LS restraints |
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