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- PDB-6a01: The crystal structure of Mandelate oxidase Y128F with 3,3-difluor... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a01 | ||||||
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Title | The crystal structure of Mandelate oxidase Y128F with 3,3-difluoro-2,2-dihydroxy-3-phenylpropionic 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 | ![]() | 89.4 KB | Display | ![]() |
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PDB format | ![]() | 64.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 770.4 KB | Display | ![]() |
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Full document | ![]() | 772.6 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5zztC ![]() 6a0bC ![]() 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-9NO / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.85 % |
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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: Mar 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 44882 / % possible obs: 99.9 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4415 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SGZ Resolution: 1.868→28.145 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.17
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.868→28.145 Å
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Refine LS restraints |
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LS refinement shell |
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