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Yorodumi- PDB-7wno: Crystallographic structure of copper amine oxidase from Arthrobac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wno | ||||||
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Title | Crystallographic structure of copper amine oxidase from Arthrobacter glibiformis at pD 7.4 determined by only neutron diffraction data. | ||||||
Components | Phenylethylamine oxidase | ||||||
Keywords | OXIDOREDUCTASE / topaquinone / TPQ | ||||||
Function / homology | Function and homology information : / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding Similarity search - Function | ||||||
Biological species | Arthrobacter globiformis (bacteria) | ||||||
Method | NEUTRON DIFFRACTION / MIR / Resolution: 1.72 Å | ||||||
Authors | Murakawa, T. / Okajima, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Iucrj / Year: 2022 Title: Re-evaluation of protein neutron crystallography with and without X-ray/neutron joint refinement. Authors: Murakawa, T. / Kurihara, K. / Adachi, M. / Kusaka, K. / 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 | 7wno.cif.gz | 327.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wno.ent.gz | 279.9 KB | Display | PDB format |
PDBx/mmJSON format | 7wno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/7wno ftp://data.pdbj.org/pub/pdb/validation_reports/wn/7wno | HTTPS FTP |
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-Related structure data
Related structure data | 7wnpC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 68993.836 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: Chemical | ChemComp-DOD / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 289 K / Method: microdialysis Details: 1.05-M potassium sodium (Na) tartrate in 25-mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||
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Diffraction source | Source: SPALLATION SOURCE / Site: JPARC MLF / Beamline: BL-03 / Type: J-PARC MLF BEAMLINE BL-03 / Wavelength: 3.0-5.7 | |||||||||
Detector | Type: iBIX / Detector: DIFFRACTOMETER / Date: Nov 10, 2015 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.72→20.94 Å / Num. obs: 76306 / % possible obs: 87.4 % / Redundancy: 2.664 % / Net I/σ(I): 4.99 | |||||||||
Reflection shell | Resolution: 1.72→1.78 Å |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.72→20.94 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 25.33 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell |
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