+Open data
-Basic information
Entry | Database: PDB / ID: 6ju8 | ||||||
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Title | Aspergillus oryzae active-tyrosinase copper-bound C92A mutant | ||||||
Components | Tyrosinase | ||||||
Keywords | OXIDOREDUCTASE / Tyrosinase / Copper enzyme / dinuclear copper center | ||||||
Function / homology | Function and homology information tyrosinase / tyrosinase activity / melanin biosynthetic process / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Aspergillus oryzae (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Fujieda, N. / Umakoshi, K. / Nishikawa, Y. / Kurisu, G. / Itoh, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Copper-Oxygen Dynamics in the Tyrosinase Mechanism. Authors: Fujieda, N. / Umakoshi, K. / Ochi, Y. / Nishikawa, Y. / Yanagisawa, S. / Kubo, M. / Kurisu, G. / Itoh, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ju8.cif.gz | 378.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ju8.ent.gz | 303.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ju8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/6ju8 ftp://data.pdbj.org/pub/pdb/validation_reports/ju/6ju8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ju4C 6ju5C 6ju6C 6ju7C 6ju9C 6juaC 6jubC 6jucC 6judC 3w6wS 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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Unit cell |
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-Components
#1: Protein | Mass: 53495.855 Da / Num. of mol.: 2 / Mutation: C92A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: OAory_01107480 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S9DK56, tyrosinase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-NO3 / | #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: 2.11 Å3/Da / Density % sol: 41.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 20% polyethylene glycol (PEG) 3350, 30mM NH4NO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→50 Å / Num. obs: 229646 / % possible obs: 99.5 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 11037 / % possible all: 96.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3W6W Resolution: 1.27→30 Å / Hydrogen treatment: constr / Cross valid method: FREE R-VALUE / σ(F): 0
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Refine analyze | Num. disordered residues: 65 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7855.2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.27→30 Å
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Refine LS restraints |
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