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- PDB-7d4d: Structure of L-lysine oxidase precursor in complex with L-lysine ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d4d | ||||||
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Title | Structure of L-lysine oxidase precursor in complex with L-lysine (1.24M) | ||||||
![]() | L-Lysine alpha-oxidase | ||||||
![]() | OXIDOREDUCTASE / L-amino acid oxidase | ||||||
Function / homology | ![]() L-amino-acid oxidase activity / amino acid catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kitagawa, M. / Ito, N. / Matsumoto, Y. / Inagaki, K. / Imada, K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of enzyme activity regulation by the propeptide of l-lysine alpha-oxidase precursor from Trichoderma viride . Authors: Kitagawa, M. / Ito, N. / Matsumoto, Y. / Saito, M. / 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 | ![]() | 124.6 KB | Display | ![]() |
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PDB format | ![]() | 91.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7d4cC ![]() 7d4eC ![]() 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 69569.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-LYS / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCl pH8.0 and 2.1 M Potassium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 26, 2017 |
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: 2.29→94.4 Å / Num. obs: 25914 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 32.17 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.056 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 4 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2533 / CC1/2: 0.861 / Rpim(I) all: 0.304 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3X0V Resolution: 2.29→75.918 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→75.918 Å
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Refine LS restraints |
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LS refinement shell |
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