+Open data
-Basic information
Entry | Database: PDB / ID: 7x7k | ||||||||||||
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Title | Ancestral L-Lys oxidase (AncLLysO-2) L-Arg binding form | ||||||||||||
Components | FAD dependent enzyme | ||||||||||||
Keywords | OXIDOREDUCTASE / L-Lys oxidase / Ancestral Sequence Reconstruction / L-Arg binding form | ||||||||||||
Function / homology | ARGININE / FLAVIN-ADENINE DINUCLEOTIDE Function and homology information | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||||||||
Authors | Motoyama, T. / Ishida, C. / Hasebe, F. / Ito, S. / Nakano, S. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Acs Omega / Year: 2022 Title: Reaction Mechanism of Ancestral l-Lys alpha-Oxidase from Caulobacter Species Studied by Biochemical, Structural, and Computational Analysis Authors: Motoyama, T. / Yamamoto, Y. / Ishida, C. / Hasebe, F. / Kawamura, Y. / Shigeta, Y. / Ito, S. / Nakano, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7x7k.cif.gz | 282.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7x7k.ent.gz | 213.9 KB | Display | PDB format |
PDBx/mmJSON format | 7x7k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/7x7k ftp://data.pdbj.org/pub/pdb/validation_reports/x7/7x7k | HTTPS FTP |
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-Related structure data
Related structure data | 7x7iSC 7x7jC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 65161.125 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 | #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: 2.12 Å3/Da / Density % sol: 42.02 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350 |
-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: Nov 1, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→45.2 Å / Num. obs: 140292 / % possible obs: 98.1 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.6→1.64 Å / Num. unique obs: 18995 / CC1/2: 0.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7X7I Resolution: 1.6→45.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.576 / SU ML: 0.055 / Cross valid method: FREE R-VALUE / ESU R: 0.086 / ESU R Free: 0.086 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: 17.941 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→45.2 Å
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Refine LS restraints |
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LS refinement shell |
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