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Yorodumi- PDB-4kff: Crystal structure of Hansenula polymorpha copper amine oxidase-1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kff | ||||||
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Title | Crystal structure of Hansenula polymorpha copper amine oxidase-1 reduced by methylamine at pH 8.5 | ||||||
Components | Peroxisomal primary amine oxidase | ||||||
Keywords | OXIDOREDUCTASE / amine oxidase / peroxisome | ||||||
Function / homology | Function and homology information : / : / : / primary-amine oxidase / amine metabolic process / quinone binding / peroxisome / copper ion binding Similarity search - Function | ||||||
Biological species | Ogataea angusta (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Johnson, B.J. / Yukl, E.T. / Klema, V.J. / Wilmot, C.M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structural evidence for the semiquinone in a copper amine oxidase from Hansenula polymorpha: implications for the catalytic mechanism Authors: Johnson, B.J. / Yukl, E.T. / Klema, V.J. / Klinman, J.P. / Wilmot, C.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kff.cif.gz | 420.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kff.ent.gz | 340.9 KB | Display | PDB format |
PDBx/mmJSON format | 4kff.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/4kff ftp://data.pdbj.org/pub/pdb/validation_reports/kf/4kff | HTTPS FTP |
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-Related structure data
Related structure data | 4kfdC 4kfeC 2oovS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 77661.617 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ogataea angusta (fungus) / Gene: AMO / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P12807, primary-amine oxidase #2: Chemical | #3: Chemical | ChemComp-GOL / #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: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 298 K / pH: 8.5 Details: 8.0-9.5% PEG8000, 0.28-0.30 M phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2005 |
Radiation | Monochromator: ROSENBAUM-ROCK HIGH-RESOLUTION 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: 2.15→50 Å / Num. obs: 122479 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.19 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OOV Resolution: 2.15→38.56 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.727 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→38.56 Å
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Refine LS restraints |
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