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Yorodumi- PDB-7rz2: Hen egg-white lysozyme with ionic liquid ethanolammonium formate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rz2 | |||||||||
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Title | Hen egg-white lysozyme with ionic liquid ethanolammonium formate 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: 1.07 Å | |||||||||
Authors | Han, Q. / Darmanin, C. / Drummond, C. / Greaves, T. | |||||||||
Funding support | 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 | 7rz2.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rz2.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7rz2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rz2_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7rz2_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7rz2_validation.xml.gz | 9 KB | Display | |
Data in CIF | 7rz2_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/7rz2 ftp://data.pdbj.org/pub/pdb/validation_reports/rz/7rz2 | HTTPS FTP |
-Related structure data
Related structure data | 7rxyC 7rydC 7rykC 7rz0C 7rz1C 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 | ChemComp-ETA / | #4: Water | ChemComp-HOH / | 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: 1.98 Å3/Da / Density % sol: 37.93 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: ethanolammonium formate 4mol% (ca. 20wt%) 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: 0.9537 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: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→24.29 Å / Num. obs: 50880 / % possible obs: 99.4 % / Redundancy: 13.4 % / CC1/2: 0.999 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.07→1.09 Å / Num. unique obs: 2520 / CC1/2: 0.91 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7JMU Resolution: 1.07→24.29 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.778 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.031 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: 10.712 Å2
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Refinement step | Cycle: LAST / Resolution: 1.07→24.29 Å
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Refine LS restraints |
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LS refinement shell |
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