+Open data
-Basic information
Entry | Database: PDB / ID: 3we0 | ||||||
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Title | L-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 | ||||||
Components | L-amino acid oxidase/monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Flavin-containing monoamine oxidase family / Rossmann Fold / Oxidoreductase (oxidase and monooxygenase) | ||||||
Function / homology | Function and homology information lysine 2-monooxygenase / lysine 2-monooxygenase activity / nucleotide binding Similarity search - Function | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Im, D.H. / Matsui, D. / Fukuta, Y. / Fushinobu, S. / Isobe, K. / Asano, Y. | ||||||
Citation | Journal: FEBS Open Bio / Year: 2014 Title: Mutational and crystallographic analysis of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813: Interconversion between oxidase and monooxygenase activities Authors: Matsui, D. / Im, D.H. / Sugawara, A. / Fukuta, Y. / Fushinobu, S. / Isobe, K. / Asano, Y. #1: Journal: J. Biosci. Bioeng. / Year: 2012 Title: Purification and characterization of an L-amino acid oxidase from Pseudomonas sp. AIU 813 Authors: Isobe, K. / Sugawara, A. / Domon, H. / Fukuta, Y. / Asano, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3we0.cif.gz | 231.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3we0.ent.gz | 183.7 KB | Display | PDB format |
PDBx/mmJSON format | 3we0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3we0_validation.pdf.gz | 933.3 KB | Display | wwPDB validaton report |
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Full document | 3we0_full_validation.pdf.gz | 960.6 KB | Display | |
Data in XML | 3we0_validation.xml.gz | 46 KB | Display | |
Data in CIF | 3we0_validation.cif.gz | 64.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/3we0 ftp://data.pdbj.org/pub/pdb/validation_reports/we/3we0 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 64516.871 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: AIU 813 / Gene: laao / Plasmid: pET15b-laao / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3IVI6*PLUS, L-amino-acid oxidase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER FOR THIS SEQUENCE IS AB830473. | |
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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: 2.47 Å3/Da / Density % sol: 50.29 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 8% polyethylene glycol (PEG) 4000, 0.1M Na-acetate(pH4.6), pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 13, 2011 |
Radiation | Monochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 101012 / Num. obs: 98486 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.082 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4930 / Rsym value: 0.507 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→30.38 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 0.002 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.961 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.951 Å / Total num. of bins used: 20
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