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- PDB-6a0b: The crystal structure of Mandelate oxidase mutant Y128F with (R)-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a0b | ||||||
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Title | The crystal structure of Mandelate oxidase mutant Y128F with (R)-3,3,3-trifluoro-2-hydroxy-propionic 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 / peroxisome / FMN binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T.L. / Lin, K.H. | ||||||
![]() | ![]() Title: Structural and chemical trapping of flavin-oxide intermediates reveals substrate-directed reaction multiplicity. Authors: Lin, K.H. / Lyu, S.Y. / Yeh, H.W. / Li, Y.S. / Hsu, N.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Wang, Z.C. / 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 | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 65.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.2 KB | Display | ![]() |
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Full document | ![]() | 793.7 KB | Display | |
Data in XML | ![]() | 18.9 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zztC ![]() 6a01C ![]() 6a1bC ![]() 6a1nC ![]() 6a1wC ![]() 6a24C ![]() 6a36C ![]() 6a3dC ![]() 6a4gC ![]() 6a4hC ![]() 7bsrC ![]() 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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1 | ![]()
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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 | ChemComp-9O0 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.68 % |
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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: Nov 4, 2016 |
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: 64008 / % possible obs: 99.6 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.019 / Net I/σ(I): 34.9 |
Reflection shell | Resolution: 1.65→1.7 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 6311 / CC1/2: 0.895 / Rpim(I) all: 0.24 / Χ2: 0.801 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SGZ Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.286 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.064 / 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: 18.313 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→30 Å
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Refine LS restraints |
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