[English] 日本語
![](img/lk-miru.gif)
- PDB-7cdm: Lysozyme room-temperature structure determined by SS-ROX combined... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7cdm | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Lysozyme room-temperature structure determined by SS-ROX combined with HAG method, 42 kGy (4500 images from 2nd half of data set) | |||||||||
![]() | Lysozyme C | |||||||||
![]() | HYDROLASE / Chicken egg white / antimicrobial enzyme / N-acetylmuramide glycanhydrolase / lysozyme-like fold | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Hasegawa, K. / Baba, S. / Kawamura, T. / Yamamoto, M. / Kumasaka, T. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Evaluation of the data-collection strategy for room-temperature micro-crystallography studied by serial synchrotron rotation crystallography combined with the humid air and glue-coating method. Authors: Hasegawa, K. / Baba, S. / Kawamura, T. / Yamamoto, M. / Kumasaka, T. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 48.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7cdkC ![]() 7cdnC ![]() 7cdoC ![]() 7cdpC ![]() 7cdqC ![]() 7cdrC ![]() 7cdsC ![]() 7cdtC ![]() 7cduC ![]() 4etaS 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
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-MLI / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: batch mode Details: The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was ...Details: The lysozyme solution (40 mg/ml) in 10 mM Na-acetate, pH 4.6 was mixed with the same volume of 4 M Na-Malonate pH 3.1, 6% w/v PEG6000 and stirred for 20 minutes. The crystal growth was stopped by adding 2.4 M Na-Malonate pH 3.1, 3.6 % w/v PEG6000. |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: Y |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→55.42 Å / Num. obs: 13831 / % possible obs: 100 % / Redundancy: 188.6 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.9766 / Net I/σ(I): 5.99 |
Reflection shell | Resolution: 1.7→1.73 Å / Num. unique obs: 664 / CC1/2: 0.5981 |
Serial crystallography sample delivery | Method: fixed target |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4eta Resolution: 1.7→55.42 Å / SU ML: 0.1808 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.6755 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→55.42 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|