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Yorodumi- PDB-5yb7: L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 -... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yb7 | ||||||
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Title | L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 - L-ornithine complex | ||||||
Components | L-amino acid oxidase/monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / L-amino acid oxidase/monooxygenase / flavin-containing monoamine oxidase family / flavin monooxygenases / L-ornithine | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. AIU 813 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Im, D. / Matsui, D. / Arakawa, T. / Isobe, K. / Asano, Y. / Fushinobu, S. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2018 Title: Ligand complex structures of l-amino acid oxidase/monooxygenase from Authors: Im, D. / Matsui, D. / Arakawa, T. / Isobe, K. / Asano, Y. / Fushinobu, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yb7.cif.gz | 457.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yb7.ent.gz | 369.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yb/5yb7 ftp://data.pdbj.org/pub/pdb/validation_reports/yb/5yb7 | HTTPS FTP |
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-Related structure data
Related structure data | 5yb6C 5yb8C 3we0S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper:
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-Components
#1: Protein | Mass: 64516.871 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. AIU 813 (bacteria) / Gene: laao, mog / Production host: Escherichia coli (E. coli) / References: UniProt: W6JQJ6 #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-ORN / #4: Water | ChemComp-HOH / | |
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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: 2.31 Å3/Da / Density % sol: 46.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% PEG 3350, 0.15 M DL-Malic acid |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 29, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→94.81 Å / Num. obs: 156339 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.779 % / Biso Wilson estimate: 37.122 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.063 / Χ2: 0.951 / Net I/σ(I): 16.01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WE0 Resolution: 2→94.81 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.285 / SU ML: 0.141 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.206 / ESU R Free: 0.175 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 124.65 Å2 / Biso mean: 36.414 Å2 / Biso min: 14.43 Å2
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Refinement step | Cycle: final / Resolution: 2→94.81 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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