[English] 日本語
![](img/lk-miru.gif)
- PDB-6yoe: Structure of Lysozyme from SiN IMISX setup collected by still ser... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6yoe | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of Lysozyme from SiN IMISX setup collected by still serial crystallography on crystals prelocated by 2D X-ray phase-contrast imaging | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / 2D X-ray phase-contrast imaging / IMISX / in situ rotation images / prelocation / still images / serial crystallography | ||||||
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, C.-Y. / Martiel, I. / Villanueva-Perez, P. / Panepucci, E. / Caffrey, M. / Wang, M. | ||||||
![]() | ![]() Title: Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography. Authors: Martiel, I. / Huang, C.Y. / Villanueva-Perez, P. / Panepucci, E. / Basu, S. / Caffrey, M. / Pedrini, B. / Bunk, O. / Stampanoni, M. / Wang, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 48.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 27 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6yobC ![]() 6yocC ![]() 6yodC ![]() 6yofC ![]() 6yogC ![]() 5d5fS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 5 types, 65 molecules ![](data/chem/img/AE3.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACY.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-AE3 / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-BR / #4: Chemical | ChemComp-NA / | #5: Chemical | ChemComp-ACY / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.44 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 4.5 Details: 0.5-1 M NaBr, 50-100 mM CH3COONa, pH 4.5, and 15-30 %(v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→55.51 Å / Num. obs: 11247 / % possible obs: 100 % / Redundancy: 11.29 % / Biso Wilson estimate: 46.37 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.26 / Net I/σ(I): 2.3 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 1101 / CC1/2: 0.22 / Rrim(I) all: 1.2 / % possible all: 96.4 |
Serial crystallography sample delivery | Method: fixed target |
Serial crystallography sample delivery fixed target | Description: IMISX / Sample dehydration prevention: SiN sandwich / Sample holding: SiN / Support base: 3D-printed holder in standard goniometer base |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5D5F Resolution: 1.85→55.51 Å / SU ML: 0.3199 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.0566
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.06 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→55.51 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|