+Open data
-Basic information
Entry | Database: PDB / ID: 3sx1 | ||||||
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Title | Hansenula polymorpha copper amine oxidase-1 in its apo form | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Klema, V.J. / Johnson, B.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 | 3sx1.cif.gz | 849.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sx1.ent.gz | 704.6 KB | Display | PDB format |
PDBx/mmJSON format | 3sx1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3sx1_validation.pdf.gz | 476.4 KB | Display | wwPDB validaton report |
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Full document | 3sx1_full_validation.pdf.gz | 492.3 KB | Display | |
Data in XML | 3sx1_validation.xml.gz | 94 KB | Display | |
Data in CIF | 3sx1_validation.cif.gz | 148 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sx/3sx1 ftp://data.pdbj.org/pub/pdb/validation_reports/sx/3sx1 | HTTPS FTP |
-Related structure data
Related structure data | 3sxxC 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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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 77632.617 Da / Num. of mol.: 3 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-GOL / #3: Chemical | ChemComp-PO4 / | #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: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 8% PEG 8000, 0.28 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: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2005 |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→50 Å / Num. all: 247478 / Num. obs: 240796 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.074 / Net I/σ(I): 32.3 |
Reflection shell | Resolution: 1.73→1.76 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.447 / % possible all: 88.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2OOV Resolution: 1.73→31.61 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.133 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R Free: 0.082 / 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: 16.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.73→31.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.732→1.777 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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