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- PDB-8d5u: Crystal structure of hen egg white lysozyme at 100 Kelvin (Triplicate) -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d5u | |||||||||
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Title | Crystal structure of hen egg white lysozyme at 100 Kelvin (Triplicate) | |||||||||
![]() | Lysozyme C | |||||||||
![]() | HYDROLASE / Antimicrobial / Bacteriolytic enzyme / Glycosidase | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Ribeiro, F.S. / Lima, L.M.T.R. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.4 KB | Display | ![]() |
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PDB format | ![]() | 27.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8d5sC ![]() 8d5tC ![]() 8d5wC ![]() 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 ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() ![]() | ||||||
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.62 % |
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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: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Oct 5, 2020 |
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54184 Å / Relative weight: 1 |
Reflection | Resolution: 1.498→22.27 Å / Num. obs: 19250 / % possible obs: 99.79 % / Redundancy: 1.9 % / CC1/2: 0.805 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.5→22.27 Å / Num. unique obs: 18264 / CC1/2: 0.805 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3A8Z Resolution: 1.498→22.268 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.205 / SU ML: 0.047 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.081 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: 10.963 Å2
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Refinement step | Cycle: LAST / Resolution: 1.498→22.268 Å
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Refine LS restraints |
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LS refinement shell |
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