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- PDB-8bbq: Determination of the structure of active tyrosinase from bacteriu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8bbq | ||||||
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Title | Determination of the structure of active tyrosinase from bacterium Verrucomicrobium spinosum | ||||||
![]() | Core tyrosinase | ||||||
![]() | METAL BINDING PROTEIN / Tyrosinase / Copper / Verrucomicrobium spinosum / PPO | ||||||
Function / homology | COPPER (II) ION![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fekry, M. / Dave, K. / Badgujar, D. / Aurelius, O. / Hamnevik, E. / Dobritzsch, D. / Danielson, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase. Authors: Fekry, M. / Dave, K.K. / Badgujar, D. / Hamnevik, E. / Aurelius, O. / Dobritzsch, D. / Danielson, U.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 153.5 KB | Display | ![]() |
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PDB format | ![]() | 118 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 43.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bbrC ![]() 4z11S ![]() 4z12S ![]() 5ce9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
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Components
#1: Protein | Mass: 36757.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-CU / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v PEG5000MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→115.2 Å / Num. obs: 62664 / % possible obs: 93.4 % / Redundancy: 6.8 % / CC1/2: 0.99 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.43→1.56 Å / Num. unique obs: 3134 / CC1/2: 0.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Z11, 4Z12, 5CE9 Resolution: 1.43→115.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.24 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 60.81 Å2 / Biso mean: 15.556 Å2 / Biso min: 8.79 Å2
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Refinement step | Cycle: final / Resolution: 1.43→115.2 Å
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Refine LS restraints NCS | Ens-ID: ens_1 / Number: 11816 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.43→1.56 Å / Rfactor Rfree error: 0
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