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Open data
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Basic information
Entry | Database: PDB / ID: 1lyo | ||||||
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Title | CROSS-LINKED LYSOZYME CRYSTAL IN NEAT WATER | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE / HYDROLASE (O-GLYCOSYL) / LYSOZYME / CROSS-LINKED | ||||||
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 | ![]() | ||||||
![]() | Huang, Q. / Wang, Z. / Zhu, G. / Qian, M. / Shao, M. / Jia, Y. / Tang, Y. | ||||||
![]() | ![]() Title: X-ray studies on cross-linked lysozyme crystals in acetonitrile-water mixture. Authors: Wang, Z. / Zhu, G. / Huang, Q. / Qian, M. / Shao, M. / Jia, Y. / Tang, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 33.5 KB | Display | ![]() |
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PDB format | ![]() | 25.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.4 KB | Display | ![]() |
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Full document | ![]() | 411.3 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2lyoC ![]() 3lyoC ![]() 4lyoC ![]() 6lytS 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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Unit cell |
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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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.3 Details: PROTEIN WAS CRYSTALLIZED FROM SODIUM ACETATE BUFFER (PH 4.3) CONTAINING 6.0% (W/V) SODIUM CHLORIDE | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 24-25 ℃ / pH: 4.1 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Dec 1, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→80 Å / Num. obs: 7746 / % possible obs: 79.4 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.2 |
Reflection | *PLUS Num. measured all: 37608 |
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Processing
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Refinement | Method to determine structure: DIRECT REFINEMENT Starting model: PDB ENTRY 6LYT Resolution: 1.93→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 2
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Displacement parameters | Biso mean: 32.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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