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Open data
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Basic information
Entry | Database: PDB / ID: 7wxs | ||||||
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Title | Lysozyme protected by polyacrylamide gel | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Hydrogel / polyacrylamide 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 | ![]() ![]() ![]() | ||||||
![]() | Muroyama, H. / Tomoike, F. / Nagae, T. / Okada, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Post-crystallization protection of protein crystals by polyacrylamide Authors: Muroyama, H. / Kato, S. / Itabashi, T. / Nagae, T. / 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 | ![]() | 53.1 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.3 KB | Display | ![]() |
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Full document | ![]() | 423.2 KB | Display | |
Data in XML | ![]() | 8.9 KB | Display | |
Data in CIF | ![]() | 12.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wxtC ![]() 6lt5S 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: NA / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-GOL / |
#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: 39.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / 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: Jun 18, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→25.02 Å / Num. obs: 32552 / % possible obs: 98.3 % / Redundancy: 6 % / Biso Wilson estimate: 9.53 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.13 / Net I/σ(I): 23.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6lt5 Resolution: 1.25→25.02 Å / SU ML: 0.0901 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.3568 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: 13.87 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→25.02 Å
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Refine LS restraints |
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LS refinement shell |
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