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- PDB-7ryk: Hen egg-white lysozyme with ionic liquid ethanolammonium nitrate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ryk | ||||||
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Title | Hen egg-white lysozyme with ionic liquid ethanolammonium nitrate 1 mol% | ||||||
![]() | Lysozyme C | ||||||
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Function / homology | ![]() Lactose synthesis / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Han, Q. / Darmanin, C. / Smith, K. / Drummond, C. / Greaves, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: Probing ion-binding at a protein interface: Modulation of protein properties by ionic liquids. Authors: Han, Q. / Su, Y. / Smith, K.M. / Binns, J. / Drummond, C.J. / Darmanin, C. / Greaves, T.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 203.9 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rxyC ![]() 7rydC ![]() 7rz0C ![]() 7rz1C ![]() 7rz2C ![]() 7jmuS C: citing same article ( S: Starting model for refinement |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NO3 / ![]() #3: 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: 1.78 Å3/Da / Density % sol: 30.75 % |
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Crystal grow![]() | Temperature: 293.15 K / Method: microbatch / pH: 8 / Details: ethanolammonium nitrate 1mol% (ca. 7wt%) in water |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.76→43.03 Å / Num. obs: 19931 / % possible obs: 99.9 % / Redundancy: 3.3 % / CC1/2: 0.996 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.76→1.8 Å / Num. unique obs: 1414 / CC1/2: 0.615 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7JMU Resolution: 1.76→29.75 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.933 / SU B: 8.506 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R Free: 0.139 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.718 Å2
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Refinement step | Cycle: LAST / Resolution: 1.76→29.75 Å
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Refine LS restraints |
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LS refinement shell |
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