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Yorodumi- PDB-3sxx: Hansenula polymorpha copper amine oxidase-1 in complex with Co(II) -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sxx | ||||||
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Title | Hansenula polymorpha copper amine oxidase-1 in complex with Co(II) | ||||||
Components | Peroxisomal primary amine oxidase | ||||||
Keywords | OXIDOREDUCTASE / peroxisome | ||||||
Function / homology | Function and homology information primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / peroxisome / copper ion binding Similarity search - Function | ||||||
Biological species | Pichia angusta (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.27 Å | ||||||
Authors | Klema, V.J. / Wilmot, C.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2012 Title: The precursor form of Hansenula polymorpha copper amine oxidase 1 in complex with CuI and CoII. Authors: Klema, V.J. / Johnson, B.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 | 3sxx.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3sxx.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 3sxx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sxx_validation.pdf.gz | 527.9 KB | Display | wwPDB validaton report |
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Full document | 3sxx_full_validation.pdf.gz | 597.7 KB | Display | |
Data in XML | 3sxx_validation.xml.gz | 205.6 KB | Display | |
Data in CIF | 3sxx_validation.cif.gz | 322.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sxx ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sxx | HTTPS FTP |
-Related structure data
Related structure data | 3sx1C 3t0uC 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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Unit cell |
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-Components
#1: Protein | Mass: 77632.617 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pichia angusta (fungus) / Gene: AMO / Production host: Escherichia coli (E. coli) / References: UniProt: P12807, primary-amine oxidase #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-GOL / #4: Chemical | #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: 2.58 Å3/Da / Density % sol: 52.28 % |
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Crystal grow | Temperature: 298 K / pH: 6 Details: 8.5% PEG 8000, 0.27 M potassium phosphate, pH 6.0, 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: 0.97945 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 8, 2007 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→50 Å / Num. obs: 1169541 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.073 / Net I/σ(I): 23.5 |
Reflection shell | Resolution: 1.27→1.32 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.357 / % possible all: 85.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ID 2OOV Resolution: 1.27→31.7 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.907 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.14 Å2
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Refinement step | Cycle: LAST / Resolution: 1.27→31.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.27→1.3 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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