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Yorodumi- PDB-8owc: Crystal structure of Hen Egg White Lysozyme co-crystallized with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8owc | ||||||
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Title | Crystal structure of Hen Egg White Lysozyme co-crystallized with 10 mM TbXo4 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / HEWL / Crystallophore / nucleating agent | ||||||
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: 1.7 Å | ||||||
Authors | Alsalman, Z. / Girard, E. | ||||||
Funding support | France, 1items
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Citation | Journal: Chemistry / Year: 2024 Title: Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network. Authors: Roux, A. / Alsalman, Z. / Jiang, T. / Mulatier, J.C. / Pitrat, D. / Dumont, E. / Riobe, F. / Gillet, N. / Girard, E. / Maury, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8owc.cif.gz | 103.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8owc.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 8owc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8owc_validation.pdf.gz | 776.3 KB | Display | wwPDB validaton report |
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Full document | 8owc_full_validation.pdf.gz | 776.5 KB | Display | |
Data in XML | 8owc_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 8owc_validation.cif.gz | 12.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/8owc ftp://data.pdbj.org/pub/pdb/validation_reports/ow/8owc | HTTPS FTP |
-Related structure data
Related structure data | 8p2qC 8piwC 8pobC C: citing same article (ref.) |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 16257.660 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, 147 molecules
#2: Chemical | ChemComp-TB / | ||||
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#3: Chemical | ChemComp-7MT / | ||||
#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: 1.73 Å3/Da / Density % sol: 28.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 650 mM sodium chloride, 100mM sodium acetate pH=4.6. Drops were set by mixing one volume of protein solution at 20mg/ml with one volume of 10mM TbXo4 and with one volume of the well solution. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.648 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 16, 2020 |
Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.648 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.49 Å / Num. obs: 13059 / % possible obs: 99.7 % / Redundancy: 24 % / Biso Wilson estimate: 27.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.026 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 23.5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 9 / Num. unique obs: 1848 / CC1/2: 0.986 / Rpim(I) all: 0.073 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→33.75 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.4769 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: 32.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.75 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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