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Open data
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Basic information
Entry | Database: PDB / ID: 8fry | ||||||
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Title | Crystal structure of hen egg white lysozyme | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Lima, L.M.T.R. / Ramos, N.G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of hen egg white lysozyme Authors: Lima, L.M.T.R. / Ramos, N.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 42.5 KB | Display | ![]() |
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PDB format | ![]() | 27.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8fp6C ![]() 8fp7C ![]() 8fp8C ![]() 8fpbC ![]() 8fpdC ![]() 8fpmC ![]() 8fpnC ![]() 8fppC ![]() 8fprC ![]() 8fpuC ![]() 8fs0C ![]() 8fs9C ![]() 8fsaC ![]() 8fscC ![]() 8fsfC ![]() 8fsgC ![]() 8fshC ![]() 8fsmC ![]() 8fsnC ![]() 8fstC ![]() 8fsuC ![]() 8fsvC ![]() 8fswC ![]() 8fsxC ![]() 8fsyC ![]() 8ft0C ![]() 8ft1C ![]() 8ft2C ![]() 8ft3C ![]() 6qwyS 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: lyzozyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 4.6 Details: 1.2 M NaCl, 100 mM Sodium Acetate, 50 mg/mL Lyzozyme, 30% Glycerol for cryoprotection |
-Data collection
Diffraction | Mean temperature: 125 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5406 Å |
Detector | Type: OXFORD TITAN CCD / Detector: CCD / Date: Sep 10, 2020 |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→13.45 Å / Num. obs: 15517 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.031 / Rrim(I) all: 0.072 / Χ2: 0.69 / Net I/σ(I): 11.9 / Num. measured all: 71288 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 99.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.579 / Num. measured all: 2246 / Num. unique obs: 777 / CC1/2: 0.769 / Rpim(I) all: 0.406 / Rrim(I) all: 0.71 / Χ2: 0.34 / Net I/σ(I) obs: 1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QWY Resolution: 1.6→13.45 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.161 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.247 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→13.45 Å
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Refine LS restraints |
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