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- PDB-3npy: Crystal Structure of Tyrosinase from Bacillus megaterium soaked i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3npy | ||||||
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Title | Crystal Structure of Tyrosinase from Bacillus megaterium soaked in CuSO4 | ||||||
![]() | Tyrosinase | ||||||
![]() | OXIDOREDUCTASE / tyrosinase / type3 copper proteins / Bacillus megaterium | ||||||
Function / homology | ![]() tyrosinase activity / melanin biosynthetic process / pigmentation / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Sendovski, M. / Kanteev, M. / Adir, N. / Fishman, A. | ||||||
![]() | ![]() Title: First structures of an active bacterial tyrosinase reveal copper plasticity. Authors: Sendovski, M. / Kanteev, M. / Shuster Ben-Yosef, V. / Adir, N. / Fishman, A. #1: ![]() Title: Crystallization and preliminary x-ray crystallographic analysis of a bacterial tyrosinase from Bacillus megaterium Authors: Sendovski, M. / Kanteev, M. / Adir, N. / Fishman, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 132.5 KB | Display | ![]() |
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PDB format | ![]() | 102.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452 KB | Display | ![]() |
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Full document | ![]() | 486.9 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 38.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3nm8SC ![]() 3nq0C ![]() 3nq1C ![]() 3nq5C ![]() 3ntmC 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
#1: Protein | Mass: 35284.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 8000, ZnAc, sodium cacodylate, pH 6.1, vapor diffusion, hanging drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.192→73.36 Å / Num. all: 31248 / Num. obs: 31000 / % possible obs: 98.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 13 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3NM8 Resolution: 2.192→50 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.098 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati sigma a obs: 0.37 Å | ||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.192→50 Å
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LS refinement shell | Resolution: 2.192→2.249 Å / Total num. of bins used: 20
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