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- PDB-6a1l: Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleot... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6a1l | ||||||
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Title | Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and 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: 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.2 KB | Display | ![]() |
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PDB format | ![]() | 66.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zzpC ![]() 5zzrC ![]() 5zzzC ![]() 6a08C ![]() 6a0vC ![]() 6a13C ![]() 6a19C ![]() 6a1hC ![]() 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: 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-9O9 / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.8 % |
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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: Jan 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 104843 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.021 / Χ2: 1.003 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 10346 / CC1/2: 0.789 / Rpim(I) all: 0.31 / Χ2: 1.003 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3SGZ Resolution: 1.4→30 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→30 Å
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Refine LS restraints |
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LS refinement shell |
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