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Open data
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Basic information
Entry | Database: PDB / ID: 8fpb | ||||||
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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 | ![]() | 43.9 KB | Display | ![]() |
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PDB format | ![]() | 28.9 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 ![]() 8fpdC ![]() 8fpmC ![]() 8fpnC ![]() 8fppC ![]() 8fprC ![]() 8fpuC ![]() 8fryC ![]() 8fs0C ![]() 8fs9C ![]() 8fsaC ![]() 8fscC ![]() 8fsfC ![]() 8fsgC ![]() 8fshC ![]() 8fsmC ![]() 8fsnC ![]() 8fstC ![]() 8fsuC ![]() 8fsvC ![]() 8fswC ![]() 8fsxC ![]() 8fsyC ![]() 8ft0C ![]() 8ft1C ![]() 8ft2C ![]() 8ft3C 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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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 / 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 | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density meas: 38.22 Mg/m3 / Density % sol: 37.81 % |
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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: 1.54056 Å |
Detector | Type: OXFORD TITAN CCD / Detector: CCD / Date: Aug 19, 2020 |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54056 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→13.54 Å / Num. obs: 15645 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC1/2: 0.975 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.056 / Rrim(I) all: 0.126 / Χ2: 0.81 / Net I/σ(I): 7 / Num. measured all: 66531 |
Reflection shell | Resolution: 1.6→1.63 Å / % possible obs: 95 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.756 / Num. measured all: 2002 / Num. unique obs: 768 / CC1/2: 0.589 / Rpim(I) all: 0.563 / Rrim(I) all: 0.948 / Χ2: 0.55 / Net I/σ(I) obs: 1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 16.206 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→13.54 Å
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Refine LS restraints |
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