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Yorodumi- PDB-7rz1: Hen egg-white lysozyme with ionic liquid ethanolammonium formate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rz1 | |||||||||
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Title | Hen egg-white lysozyme with ionic liquid ethanolammonium formate 14.4 mol% | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / lysozyme / ionic liquid / ethanolammonium formate | |||||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.046 Å | |||||||||
Authors | Han, Q. / Darmanin, C. / Drummond, C. / Greaves, T. | |||||||||
Funding support | Australia, 1items
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Citation | Journal: J Colloid Interface Sci / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rz1.cif.gz | 114.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rz1.ent.gz | 84.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rz1_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 7rz1_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7rz1_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 7rz1_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/7rz1 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rz1 | HTTPS FTP |
-Related structure data
Related structure data | 7rxyC 7rydC 7rykC 7rz0C 7rz2C 7jmuS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||||||
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.2398 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |