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- PDB-7rxy: Hen egg-white lysozyme with ionic liquid ethylammonium nitrate 5 mol% -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rxy | ||||||
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Title | Hen egg-white lysozyme with ionic liquid ethylammonium nitrate 5 mol% | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / lysozyme / ionic liquid / ethylammonium nitrate | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm 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 | ![]() | 117.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.4 MB | Display | ![]() |
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Full document | ![]() | 3.4 MB | Display | |
Data in XML | ![]() | 13.1 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rydC ![]() 7rykC ![]() 7rz0C ![]() 7rz1C ![]() 7rz2C ![]() 7jmuS 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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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: 1.79 Å3/Da / Density % sol: 31.28 % |
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Crystal grow | Temperature: 293.15 K / Method: microbatch Details: ionic liquid ethylammonium nitrate 5 mol% (ca. 24wt%) 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: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→43.14 Å / Num. obs: 26661 / % possible obs: 99.9 % / Redundancy: 3.5 % / CC1/2: 0.999 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1365 / CC1/2: 0.95 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JMU Resolution: 1.6→29.841 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.149 / SU B: 4.456 / SU ML: 0.07 / Average fsc free: 0.9323 / Average fsc work: 0.9538 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.102 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: 25.36 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→29.841 Å
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Refine LS restraints |
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LS refinement shell |
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