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- PDB-2zmy: Crystal structure of the met2-form of the copper-bound tyrosinase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2zmy | ||||||
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Title | Crystal structure of the met2-form of the copper-bound tyrosinase in complex with a caddie protein from Streptomyces castaneoglobisporus obtained by soaking in cupric sulfate solution for 80 hours | ||||||
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![]() | OXIDOREDUCTASE/METAL TRANSPORT / TYROSINASE / BINARY COMPLEX / TYPE-3 COPPER / DIOXYGEN / COPPER TRANSFER / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX / Copper / Metal-binding | ||||||
Function / homology | ![]() tyrosinase activity / melanin biosynthetic process / pigmentation / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matoba, Y. / Sugiyama, M. | ||||||
![]() | ![]() Title: X-Ray Snapshots of a Hydroxylation Mechanism of Tyrosinase Authors: Matoba, Y. / Yoshitsu, H. / Jeon, H.-J. / Oda, K. / Noda, M. / Kumagai, T. / Sugiyama, M. #1: ![]() Title: Crystallographic Evidence That the Dinuclear Copper Center of Tyrosinase Is Flexible during Catalysis Authors: Matoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / 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 | ![]() | 97.6 KB | Display | ![]() |
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PDB format | ![]() | 71.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2zmzC ![]() 1wx3 ![]() 2zn0 ![]() 2zn1 ![]() 2zn2 ![]() 2zn3 ![]() 2zn4 ![]() 2zn5 ![]() 2zn6 C: citing same article ( S: Starting model for refinement |
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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: HUT 6202 / Gene: TYRC / Plasmid: PET-MEL2 / Production host: ![]() ![]() | ||||||
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#2: Protein | Mass: 14203.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HUT 6202 / Gene: ORF378 / Plasmid: PET-MEL2 / Production host: ![]() ![]() | ||||||
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Water | ChemComp-HOH / | Sequence details | FOR THE CHAIN A, THERE IS DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. THE DEPOSITOR ...FOR THE CHAIN A, THERE IS DIFFERENCE | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 34.39 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, SODIUM NITRATE, HEPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→100 Å / Num. all: 62449 / Num. obs: 62449 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 26.5 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6161 / Rsym value: 0.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1WX3 ![]() 1wx3 Resolution: 1.45→30 Å / Num. parameters: 13136 / Num. restraintsaints: 12026 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3237 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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