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- PDB-7rz1: Hen egg-white lysozyme with ionic liquid ethanolammonium formate ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rz1 | |||||||||
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Title | Hen egg-white lysozyme with ionic liquid ethanolammonium formate 14.4 mol% | |||||||||
![]() | Lysozyme C | |||||||||
![]() | HYDROLASE / lysozyme / ionic liquid / ethanolammonium formate | |||||||||
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. / Drummond, C. / Greaves, T. | |||||||||
Funding support | ![]()
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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 | ![]() | 114.9 KB | Display | ![]() |
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PDB format | ![]() | 84.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 8.7 KB | Display | |
Data in CIF | ![]() | 11.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rxyC ![]() 7rydC ![]() 7rykC ![]() 7rz0C ![]() 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-FMT / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | The protein is a monomer, but is an oligomer in the presence of concentrated ionic liquid. Under ...The protein is a monomer, but is an oligomer in the presence of concentrated ionic liquid. Under these conditions, SAXS indicates that the radius of gyration increased to over 20 angstroms compared with 15 angstroms in buffer. | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.31 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: ethanolammonium formate 14.4mol% (ca. 50wt%) in water |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2398 Å / Relative weight: 1 |
Reflection | Resolution: 2.046→54.2 Å / Num. obs: 7613 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.981 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.05→2.1 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 571 / CC1/2: 0.852 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JMU Resolution: 2.046→54.2 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.907 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.14 / SU B: 13.824 / SU ML: 0.156 / Average fsc free: 0.9114 / Average fsc work: 0.9306 / Cross valid method: THROUGHOUT / ESU R Free: 0.207 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: 18.825 Å2
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Refinement step | Cycle: LAST / Resolution: 2.046→54.2 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -19.5967 Å / Origin y: -1.6795 Å / Origin z: -9.3171 Å
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Refinement TLS group | Selection: ALL |