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- PDB-3weu: Crystal structure of the L-Lys epsilon-oxidase from Marinomonas m... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3weu | ||||||
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Title | Crystal structure of the L-Lys epsilon-oxidase from Marinomonas mediterranea | ||||||
![]() | L-lysine 6-oxidase | ||||||
![]() | OXIDOREDUCTASE / amino acid oxidase / arm / beta barrel / three beta sheets / amine oxidase / L-Lys binding | ||||||
Function / homology | ![]() L-lysine 6-oxidase / L-lysine 6-oxidase activity / negative regulation of single-species biofilm formation / quinone binding / killing of cells of another organism / defense response to bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Okazaki, S. / Nakano, S. / Matsui, D. / Akaji, S. / Inagaki, K. / Asano, Y. | ||||||
![]() | ![]() Title: X-Ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine {varepsilon}-oxidase from Marinomonas mediterranea Authors: Okazaki, S. / Nakano, S. / Matsui, D. / Akaji, S. / Inagaki, K. / Asano, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.4 KB | Display | ![]() |
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PDB format | ![]() | 255.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 491.1 KB | Display | ![]() |
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Full document | ![]() | 507.4 KB | Display | |
Data in XML | ![]() | 61 KB | Display | |
Data in CIF | ![]() | 91.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 81010.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.6M ammonium sulfate, 10%(v/v) 1,4-dioxane, 0.1M MES/NaOH, 0.2M NaI, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 20, 2013 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 124499 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.1 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.94→1.97 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 6.8 / Num. unique all: 21819 / % possible all: 92.5 |
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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: 21.737 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→47.54 Å
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Refine LS restraints |
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