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- PDB-1wx4: Crystal structure of the oxy-form of the copper-bound Streptomyce... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1wx4 | ||||||
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Title | Crystal structure of the oxy-form of the copper-bound Streptomyces castaneoglobisporus tyrosinase complexed with a caddie protein prepared by the addition of dithiothreitol | ||||||
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![]() | OXIDOREDUCTASE/METAL TRANSPORT / tyrosinase / binary complex / type-3 copper / dioxygen / OXIDOREDUCTASE-METAL TRANSPORT COMPLEX | ||||||
Function / homology | ![]() tyrosinase activity / melanin biosynthetic process / pigmentation / copper ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Matoba, Y. / Kumagai, T. / Yamamoto, A. / Yoshitsu, H. / Sugiyama, M. | ||||||
![]() | ![]() 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 | ![]() | 92.8 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 445.4 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 27.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wx2C ![]() 1wx5C ![]() 1wxcSC ![]() 2ahkC ![]() 2ahlC ![]() 2zmxC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32089.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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.) ![]() Gene: orf378 / Plasmid: pET-mel2 / Production host: ![]() ![]() |
-Non-polymers , 4 types, 375 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/PER.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-NO3 / #5: Chemical | ChemComp-PER / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG3350, 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: MARRESEARCH / Detector: CCD / Date: Mar 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→100 Å / Num. all: 57545 / Num. obs: 57452 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.5 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.055 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.209 / Mean I/σ(I) obs: 7.7 / Num. unique all: 8285 / Rsym value: 0.189 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WXC Resolution: 1.5→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 14.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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