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- PDB-7ryd: Hen egg-white lysozyme with ionic liquid butylammonium nitrate 1 mol% -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ryd | ||||||
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Title | Hen egg-white lysozyme with ionic liquid butylammonium nitrate 1 mol% | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / lysozyme / ionic liquid / butylammonium 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 | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 3.9 MB | Display | ![]() |
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Full document | ![]() | 3.9 MB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rxyC ![]() 7rykC ![]() 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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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: 1.8 Å3/Da / Density % sol: 31.67 % |
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Crystal grow | Temperature: 298.15 K / Method: microbatch / pH: 8 / Details: butylammonium nitrate 1 mol% (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: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.18→43.18 Å / Num. obs: 67030 / % possible obs: 99.8 % / Redundancy: 6.2 % / CC1/2: 0.992 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 1.18→1.2 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3344 / CC1/2: 0.036 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JMU Resolution: 1.18→17.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.799 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.054 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: 14.338 Å2
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Refinement step | Cycle: LAST / Resolution: 1.18→17.09 Å
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Refine LS restraints |
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LS refinement shell |
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