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Open data
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Basic information
Entry | Database: PDB / ID: 6lt5 | ||||||
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Title | Lysozyme protected by alginate gel | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Hydrogel Alginate gel | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Tomoike, F. / Morita, S. / Nagae, T. / Okada, T. | ||||||
![]() | ![]() Title: Post-crystallization protection of protein crystals Authors: Morita, S. / Itabashi, T. / Nagae, T. / Takeuchi, S. / Okada, T. / Tomoike, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.1 KB | Display | ![]() |
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PDB format | ![]() | 28.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 432.7 KB | Display | ![]() |
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Full document | ![]() | 432.7 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vcgC ![]() 1dpxS 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 genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.02 % |
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Crystal grow | Temperature: 277 K / Method: counter-diffusion / pH: 4.5 / Details: 50mM sodium acetate, 1.5M NaCl, pH 4.5 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→35.37 Å / Num. obs: 29447 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.47 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 1.3→1.32 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2 / Num. unique obs: 1401 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1dpx Resolution: 1.32→30.84 Å / SU ML: 0.1206 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.5263 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: 14.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→30.84 Å
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Refine LS restraints |
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LS refinement shell |
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