+Open data
-Basic information
Entry | Database: PDB / ID: 8d5w | |||||||||
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Title | Crystal structure of hen egg white lysozyme at 125 Kelvin | |||||||||
Components | Lysozyme C | |||||||||
Keywords | HYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.499 Å | |||||||||
Authors | Ribeiro, F.S. / Lima, L.M.T.R. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Biophys.Chem. / Year: 2023 Title: Linking B-factor and temperature-induced conformational transition. Authors: de Sa Ribeiro, F. / Lima, L.M.T.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d5w.cif.gz | 45.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d5w.ent.gz | 28 KB | Display | PDB format |
PDBx/mmJSON format | 8d5w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5w ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5w | HTTPS FTP |
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-Related structure data
Related structure data | 8d5sC 8d5tC 8d5uC 8d5xC 8d5zC 8d60C 8d61C 8d62C 8d69C 8d6bC 8d6iC 8d75C 8d77C 8d7aC 8d7bC 8d7cC 8d7dC 8d7jC 8d7lC 8d7qC 8d7sC 8d8aC 8d8bC 8d8cC 8d8dC 8d8eC 8d8fC 8d8gC 8d8hC 3a8zS S: Starting model for refinement 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 1.2 M NaCl and 100 mM AcONa pH 4.6 |
-Data collection
Diffraction | Mean temperature: 125 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.54184 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Oct 7, 2020 |
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.499→22.3 Å / Num. obs: 19280 / % possible obs: 99.61 % / Redundancy: 1.89 % / CC1/2: 0.802 / Net I/σ(I): 7.17 |
Reflection shell | Resolution: 1.499→22.3 Å / Num. unique obs: 19280 / CC1/2: 0.802 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3A8Z Resolution: 1.499→22.3 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.371 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.082 / ESU R Free: 0.082 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: 10.869 Å2
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Refinement step | Cycle: LAST / Resolution: 1.499→22.3 Å
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Refine LS restraints |
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LS refinement shell |
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