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- PDB-2y9w: Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, i... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2y9w | ||||||
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Title | Crystal structure of PPO3, a tyrosinase from Agaricus bisporus, in deoxy-form that contains additional unknown lectin-like subunit | ||||||
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![]() | OXIDOREDUCTASE / COPPER-CONTAINING / PIGMENTATION / TYPE-3 COPPER PROTEIN | ||||||
Function / homology | ![]() tyrosinase / tyrosinase activity / melanin biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ismaya, W.T. / Rozeboom, H.J. / Weijn, A. / Mes, J.J. / Fusetti, F. / Wichers, H.J. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: Crystal Structure of Agaricus Bisporus Mushroom Tyrosinase: Identity of the Tetramer Subunits and Interaction with Tropolone. Authors: Ismaya, W.T. / Rozeboom, H.J. / Weijn, A. / Mes, J.J. / Fusetti, F. / Wichers, H.J. / Dijkstra, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447.1 KB | Display | ![]() |
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PDB format | ![]() | 368.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.2 KB | Display | ![]() |
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Full document | ![]() | 482.5 KB | Display | |
Data in XML | ![]() | 42 KB | Display | |
Data in CIF | ![]() | 58.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y9xC ![]() 1bt1S ![]() 1js8S ![]() 1lnlS ![]() 1wx2S 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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 45318.617 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-392 / Source method: isolated from a natural source / Details: COMMERCIAL / Source: (natural) ![]() #2: Protein | Mass: 16478.287 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: COMMERCIAL / Source: (natural) ![]() |
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-Non-polymers , 5 types, 403 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/HO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CU / #4: Chemical | ChemComp-HO / #5: Chemical | #6: Chemical | ChemComp-PGE / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.7 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 10% PEG 4000, 100 MM NA ACETATE PH 4.6, 5 MM HOLMIUM CHLORIDE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 2, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→61.1 Å / Num. obs: 53813 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDE ENTRIES 1JS8, 1LNL, 1WX2, AND 1BT1 Resolution: 2.3→47.13 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.914 / SU B: 15.1 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→47.13 Å
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Refine LS restraints |
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