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Open data
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Basic information
Entry | Database: PDB / ID: 7vgo | ||||||
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Title | Hen egg lysozyme | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / lysozyme | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Oda, M. / Ikura, T. / Ito, N. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structural Analysis of Hen Egg Lysozyme Refolded after Denaturation at Acidic pH. Authors: Oda, M. / Sano, T. / Kamatari, Y.O. / Abe, Y. / Ikura, T. / Ito, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 82.2 KB | Display | ![]() |
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PDB format | ![]() | 49.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 408.7 KB | Display | ![]() |
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Full document | ![]() | 408.7 KB | Display | |
Data in XML | ![]() | 8 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vgpC ![]() 4qeqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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 / Source: (natural) ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / #4: 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: 38.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 0.1M sodium acetate, 8%(w/v) sodium chloride, 0.1M cesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. obs: 36189 / % possible obs: 97.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 11.5 Å2 / Rsym value: 0.049 / Net I/σ(I): 66.38 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 6.28 % / Mean I/σ(I) obs: 6.8 / Num. unique obs: 1522 / CC1/2: 0.941 / Rsym value: 0.383 / % possible all: 84.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4QEQ Resolution: 1.2→25.49 Å / SU ML: 0.0749 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.7556 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.34 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.2→25.49 Å
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Refine LS restraints |
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LS refinement shell |
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