[English] 日本語
![](img/lk-miru.gif)
- PDB-1wqr: CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1wqr | ||||||
---|---|---|---|---|---|---|---|
Title | CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE / HYDROLASE (O-GLYCOSYL) / GLYCOSIDASE / BACTERIOLYTIC ENZYME | ||||||
Function / homology | ![]() antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...antimicrobial humoral response / Antimicrobial peptides / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Yamagata, Y. / Kubota, M. / Sumikawa, Y. / Funahashi, J. / Fujii, S. / Yutani, K. | ||||||
![]() | ![]() Title: Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six tyrosine --> phenylalanine mutants. Authors: Yamagata, Y. / Kubota, M. / Sumikawa, Y. / Funahashi, J. / Takano, K. / Fujii, S. / Yutani, K. #1: ![]() Title: Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants Authors: Takano, K. / Yamagata, Y. / Fujii, S. / Yutani, K. #2: ![]() Title: Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability Authors: Takano, K. / Funahashi, J. / Yamagata, Y. / Fujii, S. / Yutani, K. #3: ![]() Title: Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants Authors: Takano, K. / Ogasahara, K. / Kaneda, H. / Yamagata, Y. / Fujii, S. / Kanaya, E. / Kikuchi, M. / Oobatake, M. / Yutani, K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 42 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 28.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 14704.693 Da / Num. of mol.: 1 / Mutation: Y63F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-NA / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.5 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.5 / Details: 1.6M TO 1.9M NACL, 20MM ACETATE, PH 4.5 | ||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 10 ℃ / Method: vapor diffusion, hanging drop / Details: Takano, K., (1995) J.Mol.Biol., 254, 62. | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 283 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 14, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.586→56.7 Å / Num. obs: 48753 / % possible obs: 86.8 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.586→1.7 Å / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.89 / % possible all: 72.6 |
Reflection | *PLUS Num. obs: 14363 / Num. measured all: 48753 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: DIFFERENCE MAP Starting model: WILD-TYPE OF HUMAN LYSOZYME Resolution: 1.8→8 Å / σ(F): 3
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.88 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|