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Open data
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Basic information
Entry | Database: PDB / ID: 6a1w | |||||||||
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Title | Mandelate oxidase with the enoyl FMN epoxide adduct | |||||||||
![]() | 4-hydroxymandelate oxidase![]() | |||||||||
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Function / homology | ![]() ![]() 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 | ![]() | 93.9 KB | Display | ![]() |
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PDB format | ![]() | 66.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5zztC ![]() 6a01C ![]() 6a0bC ![]() 6a1bC ![]() 6a1nC ![]() 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: 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-MG / |
#3: Chemical | ChemComp-9P3 / |
#4: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.88 % |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Aug 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→30 Å / Num. obs: 58282 / % possible obs: 99 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.018 / Χ2: 0.946 / Net I/σ(I): 34.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5775 / CC1/2: 0.803 / Rpim(I) all: 0.25 / Χ2: 0.787 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 3SGZ Resolution: 1.7→26.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.631 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.21 Å2 / Biso mean: 20.096 Å2 / Biso min: 3.89 Å2
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Refinement step | Cycle: final / Resolution: 1.7→26.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.701→1.745 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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