[English] 日本語
![](img/lk-miru.gif)
- PDB-9lyz: X-RAY CRYSTALLOGRAPHY OF THE BINDING OF THE BACTERIAL CELL WALL T... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 9lyz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-RAY CRYSTALLOGRAPHY OF THE BINDING OF THE BACTERIAL CELL WALL TRISACCHARIDE NAM-NAG-NAM TO LYSOZYME | |||||||||
![]() | HEN EGG WHITE LYSOZYME | |||||||||
![]() | HYDROLASE (O-GLYCOSYL) | |||||||||
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 | ![]() | |||||||||
![]() | Kelly, J.A. / James, M.N.G. | |||||||||
![]() | ![]() Title: X-ray crystallography of the binding of the bacterial cell wall trisaccharide NAM-NAG-NAM to lysozyme. Authors: Kelly, J.A. / Sielecki, A.R. / Sykes, B.D. / James, M.N. / Phillips, D.C. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 37.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 28.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.5 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 472.8 KB | Display | |
Data in XML | ![]() | 8.1 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|---|
#2: Polysaccharide | N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.88 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS pH: 4.5 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 3652 / Rmerge(I) obs: 0.12 |
-
Processing
Refinement | Rfactor Rwork: 0.23 / Highest resolution: 2.5 Å Details: THIS ENTRY ORIGINALLY CONTAINED ONLY THE COORDINATES OF THE THREE SUGARS. IN ORDER TO BRING COMPLETENESS TO THE STRUCTURE, THE ENTRY HAS BEEN REMEDIATED BY MERGING THE COORDINATES OF THE ...Details: THIS ENTRY ORIGINALLY CONTAINED ONLY THE COORDINATES OF THE THREE SUGARS. IN ORDER TO BRING COMPLETENESS TO THE STRUCTURE, THE ENTRY HAS BEEN REMEDIATED BY MERGING THE COORDINATES OF THE POLYMER CHAIN AND WATER FROM THE RELATED ENTRY 6LYZ. | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
| ||||||||||||
Refinement | *PLUS Rfactor obs: 0.23 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |