[English] 日本語
![](img/lk-miru.gif)
- PDB-1ljh: CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE OF 5% ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ljh | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF MONOCLINIC LYSOZYME GROWN IN PRESENCE OF 5% GLYCEROL | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Hydration of Proteins | ||||||
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 | ![]() | ||||||
![]() | Saraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M. | ||||||
![]() | ![]() Title: Effect of stabilizing additives on the structure and hydration of proteins: a study involving monoclinic lysozyme. Authors: Saraswathi, N.T. / Sankaranarayanan, R. / Vijayan, M. #1: ![]() Title: The Effect of Stabilizing Additives on the Structure and Hydration of Proteins: A Study Involving Tetragonal Lysozyme Authors: Datta, S. / Biswal, B.K. / Vijayan, M. #2: ![]() Title: An X-Ray Analysis of Native Monoclinic Lysozyme. A Case Study on the Reliability of Refined Protein Structures and a Comparison with the Low-Humidity Form in Relation to Mobility and Enzyme Action Authors: Nagendra, H.G. / Sudarsanakumar, C. / Vijayan, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 66 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 52.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 455 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 24.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1lj3C ![]() 1lj4C ![]() 1ljeC ![]() 1ljfC ![]() 1ljgC ![]() 1ljiC ![]() 1ljjC ![]() 1ljkC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||
2 | ![]()
| ||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.32 % | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 4.6 Details: Sodium Acetate(0.1M)-Buffer, Sodium Nitrate (0.44M)-Precipitant, glycerol(0.54M) - Additive, pH 4.6, LIQUID DIFFUSION at 293K | ||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 18746 / Biso Wilson estimate: 21.1 Å2 |
Reflection shell | Resolution: 1.8→1.86 Å |
Reflection | *PLUS Highest resolution: 1.8 Å / Num. obs: 18861 / % possible obs: 97.2 % / Num. measured all: 114902 / Rmerge(I) obs: 0.046 |
Reflection shell | *PLUS % possible obs: 95.1 % / Num. unique obs: 1862 / Rmerge(I) obs: 0.139 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.8→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 820918.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.8121 Å2 / ksol: 0.363625 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|