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- PDB-5z0d: 1.16 A-resolution crystal structure of the deoxy-form tyrosinase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z0d | ||||||
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Title | 1.16 A-resolution crystal structure of the deoxy-form tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein | ||||||
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![]() | OXIDOREDUCTASE/METAL BINDING PROTEIN / tyrosinase / catalytic mechanism / OXIDOREDUCTASE-METAL BINDING PROTEIN complex | ||||||
Function / homology | ![]() tyrosinase activity / melanin biosynthetic process / pigmentation / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matoba, Y. / Sugiyama, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Catalytic mechanism of tyrosinase implied from the quinone formation on the Tyr98 residue of the caddie protein Authors: Matoba, Y. / Sugiyama, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 177.3 KB | Display | ![]() |
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PDB format | ![]() | 136.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5z0eC ![]() 5z0fC ![]() 5z0gC ![]() 5z0hC ![]() 5z0iC ![]() 5z0jC ![]() 5z0kC ![]() 5z0lC ![]() 5z0mC ![]() 1wxcS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 32089.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HUT6202 / Gene: tyrC / Plasmid: pET-mel2 / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 14089.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HUT6202 / Gene: orf378 / Plasmid: pET-mel2 / Production host: ![]() ![]() | ||||
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.94 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: PEG 3350, SODIUM NITRATE, HEPES, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 14, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→50 Å / Num. obs: 118873 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.16→1.2 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 2.9 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1wxc Resolution: 1.16→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3239.99 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→30 Å
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Refine LS restraints |
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