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Yorodumi- PDB-7bb1: Lysozyme crystallized in the presence of the hydrated deep eutect... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bb1 | |||||||||
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Title | Lysozyme crystallized in the presence of the hydrated deep eutectic solvent Choline chloride-Glutamic acid 2:1 | |||||||||
Components | Lysozyme | |||||||||
Keywords | HYDROLASE / complex / lysozyme / hydrated deep eutectic solvents | |||||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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: 1.3 Å | |||||||||
Authors | Belviso, B.D. / Caliandro, R. / Carrozzini, B. | |||||||||
Funding support | European Union, Italy, 2items
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Citation | Journal: Acs Sustain Chem Eng / Year: 2021 Title: Introducing Protein Crystallization in Hydrated Deep Eutectic Solvents Authors: Belviso, B.D. / Perna, F.M. / Carrozzini, B. / Trotta, M. / Capriati, V. / Caliandro, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bb1.cif.gz | 101.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bb1.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 7bb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/7bb1 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/7bb1 | HTTPS FTP |
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-Related structure data
Related structure data | 7b9jC 7bazC 4n9rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 5 types, 231 molecules
#2: Chemical | ChemComp-ACT / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-NA / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: sodium chloride, sodium acetate, DES: Choline chloride/Glutamic acid |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 293 / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→27.918 Å / Num. obs: 29313 / % possible obs: 99.6 % / Redundancy: 21.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.019 / Rrim(I) all: 0.092 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 1.3→1.324 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 1464 / CC1/2: 0.934 / Rpim(I) all: 0.128 / Rrim(I) all: 0.357 / % possible all: 94.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4n9r Resolution: 1.3→27.918 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 12.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.48 Å2 / Biso mean: 13.8531 Å2 / Biso min: 5.08 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→27.918 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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