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- PDB-6rrp: Crystal structure of tyrosinase PvdP from Pseudomonas aeruginosa ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6rrp | ||||||
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Title | Crystal structure of tyrosinase PvdP from Pseudomonas aeruginosa bound to copper and phenylthiourea | ||||||
![]() | PvdP | ||||||
![]() | OXIDOREDUCTASE / tyrosinase / pyoverdine / copper / inhibitor / phenylthiourea | ||||||
Function / homology | pyoverdine biosynthetic process / tyrosinase activity / Di-copper centre-containing domain superfamily / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / metal ion binding / COPPER (II) ION / N-PHENYLTHIOUREA / PvdP![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Wibowo, J.P. / Batista, F.A. / van Oosterwijk, N. / Groves, M.R. / Dekker, F.J. / Quax, W.J. | ||||||
![]() | ![]() Title: A novel mechanism of inhibition by phenylthiourea on PvdP, a tyrosinase synthesizing pyoverdine of Pseudomonas aeruginosa. Authors: Wibowo, J.P. / Batista, F.A. / van Oosterwijk, N. / Groves, M.R. / Dekker, F.J. / Quax, W.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.2 KB | Display | ![]() |
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PDB format | ![]() | 159 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 33.9 KB | Display | |
Data in CIF | ![]() | 48.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rrqC ![]() 6rrrSC 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: 62382.105 Da / Num. of mol.: 2 / Fragment: PvdP Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: pvdP, PA2392 / Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CU / #4: 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: 2.64 Å3/Da / Density % sol: 53.32 % / Mosaicity: 0.16 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% PEG 3350, 0.1M Bis-Tris Propane |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2017 / Details: KB | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 44062 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.049 / Rrim(I) all: 0.097 / Net I/σ(I): 10.9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RRR Resolution: 2.4→49.56 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.211 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.4 / ESU R Free: 0.267 / 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: 157.46 Å2 / Biso mean: 44.657 Å2 / Biso min: 18.28 Å2
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Refinement step | Cycle: final / Resolution: 2.4→49.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.459 Å / Rfactor Rfree error: 0
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