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Open data
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Basic information
Entry | Database: PDB / ID: 5zzs | ||||||
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Title | The crystal structure of Mandelate oxidase 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 | ![]() | 93.6 KB | Display | ![]() |
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PDB format | ![]() | 67.7 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 ![]() 5zzxC ![]() 5zzyC ![]() 6a00C ![]() 6a0dC ![]() 6a0gC ![]() 6a0mC ![]() 6a0oC ![]() 6a0yC ![]() 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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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 | #3: Chemical | ChemComp-FMN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.48 Å3/Da / Density % sol: 64.69 % |
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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: Jul 29, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.398→30 Å / Num. obs: 104389 / % possible obs: 99 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.398→1.45 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 10392 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SGZ Resolution: 1.398→30 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.24
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.398→30 Å
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Refine LS restraints |
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LS refinement shell |
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