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- PDB-7cit: Crystal structure of tyrosinase from Streptomyces castaneoglobisp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cit | ||||||
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Title | Crystal structure of tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the solution containing Cu(II) and hydroxylamine for 24 h | ||||||
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![]() | METAL BINDING PROTEIN / tyrosinase / catalytic mechanism | ||||||
Function / homology | COPPER (II) ION / NITRATE ION / HYDROGEN PEROXIDE![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Tyr98 residue of caddie is partially oxygenated | ||||||
![]() | Oda, K. / Matoba, Y. | ||||||
![]() | ![]() Title: The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity. Authors: Matoba, Y. / Oda, K. / Muraki, Y. / Masuda, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.1 KB | Display | ![]() |
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PDB format | ![]() | 136 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.9 MB | Display | ![]() |
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Full document | ![]() | 4.9 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 28.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ciyC ![]() 2zmyS 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
-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.) ![]() Strain: HUT 6202 / Plasmid: PET-MEL2 / Production host: ![]() ![]() |
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#2: Protein | Mass: 14217.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HUT 6202 / Plasmid: PET-MEL2 / Production host: ![]() ![]() |
-Non-polymers , 4 types, 335 molecules ![](data/chem/img/PEO.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CU.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PEO / | ||||
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#4: Chemical | ChemComp-CU / #5: Chemical | ChemComp-NO3 / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 32.61 % / Mosaicity: 0.824 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, NaNO3 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 17, 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: 1.5→100 Å / Num. obs: 53168 / % possible obs: 96.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.049 / Χ2: 0.982 / Net I/σ(I): 35.6 |
Reflection shell | Resolution: 1.5→1.55 Å / Rmerge(I) obs: 0.432 / Num. unique obs: 5762 / Χ2: 1.176 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2ZMY Resolution: 1.5→30 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.37 Å2 / Biso mean: 25.7909 Å2 / Biso min: 12.19 Å2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→30 Å
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Refine LS restraints |
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