+Open data
-Basic information
Entry | Database: PDB / ID: 3x0v | ||||||
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Title | Structure of L-lysine oxidase | ||||||
Components | L-lysine oxidase | ||||||
Keywords | OXIDOREDUCTASE / oxidative deamination / secreted protein | ||||||
Function / homology | Function and homology information L-lysine oxidase / L-lysine oxidase activity / amino acid catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Trichoderma viride (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Sano, T. / Uchida, Y. / Amano, M. / Kawaguchi, T. / Kondo, H. / Inagaki, K. / Imada, K. | ||||||
Citation | Journal: J.Biochem. / Year: 2015 Title: Recombinant expression, molecular characterization and crystal structure of antitumor enzyme, l-lysine alpha-oxidase from Trichoderma viride. Authors: Amano, M. / Mizuguchi, H. / Sano, T. / Kondo, H. / Shinyashiki, K. / Inagaki, J. / Tamura, T. / Kawaguchi, T. / Kusakabe, H. / Imada, K. / Inagaki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3x0v.cif.gz | 232.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3x0v.ent.gz | 184.5 KB | Display | PDB format |
PDBx/mmJSON format | 3x0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/3x0v ftp://data.pdbj.org/pub/pdb/validation_reports/x0/3x0v | HTTPS FTP |
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-Related structure data
Related structure data | 3kveS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 60974.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trichoderma viride (fungus) / Strain: Y244-2 / References: UniProt: A0A0J9X1X3*PLUS, L-lysine oxidase #2: Chemical | #3: Chemical | ChemComp-EPE / #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 2% (w/v) PEG 400, 0.1M HEPES pH7.6, 1.8M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2012 |
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: 1.9→34.4 Å / Num. all: 92177 / Num. obs: 92177 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 3.4 / Num. unique all: 13448 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3KVE Resolution: 1.9→32.023 Å / SU ML: 0.4 / σ(F): 1.4 / Phase error: 17.3 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.23 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→32.023 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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