+Open data
-Basic information
Entry | Database: PDB / ID: 7eii | ||||||||||||
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Title | Ancestral L-Lys oxidase K387A variant (L-Lys binding form) | ||||||||||||
Components | FAD dependent L-Lys oxidase | ||||||||||||
Keywords | OXIDOREDUCTASE / L-Lys oxidase | ||||||||||||
Function / homology | FLAVIN-ADENINE DINUCLEOTIDE / LYSINE Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||||||||
Authors | Sugiura, S. / Nakano, S. / Niwa, M. / Hasebe, F. / Ito, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2021 Title: Catalytic mechanism of ancestral L-lysine oxidase assigned by sequence data mining. Authors: Sugiura, S. / Nakano, S. / Niwa, M. / Hasebe, F. / Matsui, D. / Ito, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eii.cif.gz | 263.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eii.ent.gz | 202.1 KB | Display | PDB format |
PDBx/mmJSON format | 7eii.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7eii ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7eii | HTTPS FTP |
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-Related structure data
Related structure data | 7eihSC 7eijC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 68633.367 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-LYS / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.2 Å3/Da / Density % sol: 44.16 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 25%(w/v) PEG3350, 0.1 M Tris-HCl (pH 8.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 23, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→42.9 Å / Num. obs: 46762 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.4→2.53 Å / Rmerge(I) obs: 0.421 / Num. unique obs: 6740 / CC1/2: 0.926 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EIH Resolution: 2.4→42.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.56 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.669 / ESU R Free: 0.267 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.543 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→42.9 Å
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Refine LS restraints |
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LS refinement shell |
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