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- PDB-7c3l: Structure of L-lysine oxidase D212A/D315A in complex with L-tyrosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 7c3l | ||||||
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Title | Structure of L-lysine oxidase D212A/D315A in complex with L-tyrosine | ||||||
![]() | L-lysine oxidase | ||||||
![]() | OXIDOREDUCTASE / L-amino acid oxidase | ||||||
Function / homology | ![]() L-lysine oxidase / L-lysine oxidase activity / L-amino-acid oxidase activity / amino acid catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kitagawa, M. / Matsumoto, Y. / Inagaki, K. / Imada, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of strict substrate recognition of l-lysine alpha-oxidase from Trichoderma viride. Authors: Kondo, H. / Kitagawa, M. / Matsumoto, Y. / Saito, M. / Amano, M. / Sugiyama, S. / Tamura, T. / Kusakabe, H. / Inagaki, K. / Imada, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 273.6 KB | Display | ![]() |
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PDB format | ![]() | 197.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7c3hC ![]() 7c3iC ![]() 7c3jC ![]() 3x0vS 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60787.598 Da / Num. of mol.: 2 / Mutation: D212A,D315A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0J9X1X3, UniProt: A0A0G4DCU0*PLUS, L-lysine oxidase |
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-Non-polymers , 5 types, 1357 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/TYR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TYR.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1% (w/v) PEG400, 0.1 M Tris-HCl pH7.5, 2.1 M Ammonium Sulfate |
-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: Jul 14, 2018 |
Radiation | Monochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→75.3 Å / Num. obs: 111001 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 17.03 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 5 / Num. unique obs: 5429 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3X0V Resolution: 1.8→69.58 Å / SU ML: 0.1711 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8207 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→69.58 Å
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Refine LS restraints |
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LS refinement shell |
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