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Yorodumi- PDB-6tvy: Structure of hen egg white lysozyme crystallized in the presence ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tvy | ||||||||||||||||||
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Title | Structure of hen egg white lysozyme crystallized in the presence of Tb-Xo4 crystallophore in the XtalController device | ||||||||||||||||||
Components | Lysozyme C | ||||||||||||||||||
Keywords | ANTIMICROBIAL PROTEIN / Glycosidase / Hydrolase / beta-N-acetylglucosaminidase | ||||||||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||||||||||||||
Authors | de Wijn, R. / Rollet, K. / Coudray, L. / McEwen, A.G. / Lorber, B. / Sauter, C. | ||||||||||||||||||
Funding support | France, 5items
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Citation | Journal: Crystals / Year: 2020 Title: Monitoring the Production of High Diffraction-Quality Crystals of Two Enzymes in Real Time Using In Situ Dynamic Light Scattering Authors: de Wijn, R. / Rollet, K. / Engilberge, S. / McEwen, A.G. / Hennig, O. / Betat, H. / Moerl, M. / Riobe, F. / Maury, O. / Girard, E. / Benas, P. / Lorber, B. / Sauter, C. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tvy.cif.gz | 78.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tvy.ent.gz | 51.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/6tvy ftp://data.pdbj.org/pub/pdb/validation_reports/tv/6tvy | HTTPS FTP |
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-Related structure data
Related structure data | 6tvzC 6f2iS 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
-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, 60 molecules
#2: Chemical | ChemComp-NA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-7MT / | #5: Chemical | #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: 2.08 Å3/Da / Density % sol: 40.8 % / Description: Classical prismatic HEWL crystal |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: Lysozyme stock solution at 50 mg/ml in 10 mM Sodium Acetate pH 4.5, 40 mM NaCl, incubated in the XtalController instrument. The crystallization was triggered by the addition of 10mM Tb-Xo4 crystallophore. Temp details: +/_ 0.1 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 3, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→35.24 Å / Num. obs: 36571 / % possible obs: 99.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 1 / Rrim(I) all: 0.036 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.51→1.6 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 5936 / CC1/2: 0.78 / Rrim(I) all: 0.726 / % possible all: 96.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6f2i Resolution: 1.51→35.24 Å / SU ML: 0.1635 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.9551 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 30.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.51→35.24 Å
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Refine LS restraints |
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LS refinement shell |
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