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Yorodumi- PDB-7f8k: Room temperature structure of bacterial copper amine oxidase dete... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f8k | ||||||
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Title | Room temperature structure of bacterial copper amine oxidase determined by serial femtosecond crystallography | ||||||
Components | Phenylethylamine oxidase | ||||||
Keywords | OXIDOREDUCTASE / topaquinone copper serial femtosecond X-ray crystallography radiation-damage-free | ||||||
Function / homology | Function and homology information primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding Similarity search - Function | ||||||
Biological species | Arthrobacter globiformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MIR / Resolution: 2.2 Å | ||||||
Authors | Murakawa, T. / Okajima, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase Authors: Murakawa, T. / Suzuki, M. / Arima, T. / Sugahara, M. / Tanaka, T. / Tanaka, R. / Iwata, S. / Nango, E. / Tono, K. / Hayashi, H. / Fukui, K. / Yano, T. / Tanizawa, K. / Okajima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f8k.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f8k.ent.gz | 108.7 KB | Display | PDB format |
PDBx/mmJSON format | 7f8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f8k_validation.pdf.gz | 428 KB | Display | wwPDB validaton report |
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Full document | 7f8k_full_validation.pdf.gz | 430.5 KB | Display | |
Data in XML | 7f8k_validation.xml.gz | 24.2 KB | Display | |
Data in CIF | 7f8k_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/7f8k ftp://data.pdbj.org/pub/pdb/validation_reports/f8/7f8k | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 70752.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46881, primary-amine oxidase |
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#2: Chemical | ChemComp-CU / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.86 % |
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Crystal grow | Temperature: 289 K / Method: batch mode / pH: 7.4 Details: 1.05 M potassium-sodium tartrate in 25 mM HEPES buffer |
-Data collection
Diffraction | Mean temperature: 300 K / Serial crystal experiment: N |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL2 / Wavelength: 1.771 Å |
Detector | Type: MPCCD / Detector: CCD / Date: Jun 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.771 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 87284 / % possible obs: 100 % / Redundancy: 147.3 % / Biso Wilson estimate: 49.62 Å2 / CC1/2: 0.9858935 / Net I/σ(I): 7.76 |
Reflection shell | Resolution: 2.2→2.278 Å / Num. unique obs: 8717 / CC1/2: 0.6180976 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.2→19.96 Å / SU ML: 0.2447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1957 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.79 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→19.96 Å
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Refine LS restraints |
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LS refinement shell |
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