+Open data
-Basic information
Entry | Database: PDB / ID: 6ezz | ||||||
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Title | Crystal structure of Escherichia coli amine oxidase mutant E573Q | ||||||
Components | Primary amine oxidasePrimary-amine oxidase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information phenylethylamine catabolic process / primary amine oxidase activity / : / : / : / primary-amine oxidase / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space ...phenylethylamine catabolic process / primary amine oxidase activity / : / : / : / primary-amine oxidase / L-phenylalanine catabolic process / amine metabolic process / quinone binding / periplasmic space / copper ion binding / calcium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å | ||||||
Authors | Gaule, T.G. / Smith, M.A. / Tych, K.M. / Pirrat, P. / Trinh, C.H. / Pearson, A.R. / Knowles, P.F. / McPherson, M.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: Oxygen Activation Switch in the Copper Amine Oxidase of Escherichia coli. Authors: Gaule, T.G. / Smith, M.A. / Tych, K.M. / Pirrat, P. / Trinh, C.H. / Pearson, A.R. / Knowles, P.F. / McPherson, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ezz.cif.gz | 318.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ezz.ent.gz | 254.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ezz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/6ezz ftp://data.pdbj.org/pub/pdb/validation_reports/ez/6ezz | HTTPS FTP |
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-Related structure data
Related structure data | 6grrC 1dyuS 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: 81335.750 Da / Num. of mol.: 2 / Mutation: E573Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: tynA, maoA, b1386, JW1381 / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 blue / References: UniProt: P46883, primary-amine oxidase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.78 Å3/Da / Density % sol: 55.82 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M Sodium citrate, 100mM HEPES pH 6-7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 5, 2012 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→72.12 Å / Num. obs: 167221 / % possible obs: 99.31 % / Redundancy: 4.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.027 / Rrim(I) all: 0.061 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7889 / CC1/2: 0.806 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1DYU Resolution: 1.8→72.12 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 3.115 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.824 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→72.12 Å
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Refine LS restraints |
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