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Open data
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Basic information
Entry | Database: PDB / ID: 5zzp | ||||||
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Title | The crystal structure of Mandelate oxidase | ||||||
![]() | 4-hydroxymandelate oxidase![]() | ||||||
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Function / homology | ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Li, T.L. / Lin, K.H. | ||||||
![]() | ![]() Title: The flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level. Authors: Lyu, S.Y. / Lin, K.H. / Yeh, H.W. / Li, Y.S. / Huang, C.M. / Wang, Y.L. / Shih, H.W. / Hsu, N.S. / Wu, C.J. / Li, T.L. #1: ![]() 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 | ![]() | 94.5 KB | Display | ![]() |
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PDB format | ![]() | 68.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zzrC ![]() 5zzzC ![]() 6a08C ![]() 6a0vC ![]() 6a13C ![]() 6a19C ![]() 6a1hC ![]() 6a1lC ![]() 6a1mC ![]() 6a1pC ![]() 6a1rC ![]() 6a21C ![]() 6a23C ![]() 6a3tC ![]() 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: 40045.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FMN / ![]() |
#3: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.87 % |
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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: 200 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jul 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.389→30 Å / Num. obs: 108028 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 36.07 |
Reflection shell | Resolution: 1.389→1.44 Å / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 2.43 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3SGZ Resolution: 1.39→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.795 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.045 / 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: 18.677 Å2
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Refinement step | Cycle: 1 / Resolution: 1.39→30 Å
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Refine LS restraints |
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