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Open data
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Basic information
Entry | Database: PDB / ID: 7s2v | ||||||
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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: The reproducible normality of the crystallographic B-factor. Authors: Ramos, N.G. / Sarmanho, G.F. / de Sa Ribeiro, F. / de Souza, V. / 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 | ![]() | 43.8 KB | Display | ![]() |
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PDB format | ![]() | 28.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7s27C ![]() 7s28C ![]() 7s29C ![]() 7s2aC ![]() 7s2bC ![]() 7s2cC ![]() 7s2dC ![]() 7s2eC ![]() 7s2fC ![]() 7s2gC ![]() 7s2qC ![]() 7s2uC ![]() 7s2wC ![]() 7s30C ![]() 7s31C ![]() 7s32C ![]() 7s33C ![]() 7s34C ![]() 7s35C ![]() 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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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 natural source / Details: egg white / Source: (natural) ![]() ![]() |
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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: 1.94 Å3/Da / Density % sol: 36.67 % / Mosaicity: 1.05 ° |
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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: Dec 12, 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→13.41 Å / Num. obs: 15331 / % possible obs: 99.3 % / Redundancy: 5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.3 / Num. measured all: 76667 / Scaling rejects: 332 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6qwy Resolution: 1.6→13.41 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2318 / WRfactor Rwork: 0.1857 / FOM work R set: 0.8345 / SU B: 2.14 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1048 / SU Rfree: 0.1059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: isomorphous replacement with REFMAC , restrained refinement with REFMAC, real space refinement with C.O.O.T.
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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 max: 53.7 Å2 / Biso mean: 16.408 Å2 / Biso min: 4.41 Å2
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Refinement step | Cycle: final / Resolution: 1.6→13.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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