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- PDB-8ot8: Alditol oxidase from Actinomycetota bacterium in complex with D-x... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8ot8 | ||||||
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Title | Alditol oxidase from Actinomycetota bacterium in complex with D-xylulose | ||||||
![]() | FAD-binding protein | ||||||
![]() | FLAVOPROTEIN / Alditol oxidase / xylulose | ||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / D-XYLULOSE / : ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rotilio, L. / Mattevi, A. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Discovery and biochemical characterization of thermostable glycerol oxidases. Authors: Santema, L.L. / Rotilio, L. / Xiang, R. / Tjallinks, G. / Guallar, V. / Mattevi, A. / Fraaije, M.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 321 KB | Display | ![]() |
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PDB format | ![]() | 260.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 58.2 KB | Display | |
Data in CIF | ![]() | 78.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46176.086 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A2W4MPG3 #2: Chemical | ChemComp-FAD / #3: Sugar | ChemComp-XUL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12 M Monosaccharides 0.1 M Buffer System 2 7.5 30 % v/v Precipitant Mix 1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→49.55 Å / Num. obs: 73369 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.071 / Rrim(I) all: 0.183 / Χ2: 1.04 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 2.4→2.45 Å / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.581 / Num. measured all: 30175 / Num. unique obs: 4513 / CC1/2: 0.587 / Rpim(I) all: 1.071 / Rrim(I) all: 2.798 / Χ2: 0.98 / Net I/σ(I) obs: 0.9 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 67.423 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→49.55 Å
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Refine LS restraints |
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