[English] 日本語
![](img/lk-miru.gif)
- PDB-1n7p: Streptococcus pneumoniae Hyaluronate Lyase W292A/F343V Double Mutant -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1n7p | ||||||
---|---|---|---|---|---|---|---|
Title | Streptococcus pneumoniae Hyaluronate Lyase W292A/F343V Double Mutant | ||||||
![]() | HYALURONIDASE | ||||||
![]() | LYASE / protein mutant | ||||||
Function / homology | ![]() hyaluronate lyase / hyaluronate lyase activity / : / hydrolase activity, acting on glycosyl bonds / carbohydrate binding / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J. | ||||||
![]() | ![]() Title: The function of hydrophobic residues in the catalytic cleft of Streptococcus pneumoniae hyaluronate lyase. Kinetic characterization of mutant enzyme forms Authors: Nukui, M. / Taylor, K.B. / McPherson, D.T. / Shigenaga, M. / Jedrzejas, M.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 171.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 442.2 KB | Display | |
Data in XML | ![]() | 34.1 KB | Display | |
Data in CIF | ![]() | 52.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1n7nC ![]() 1n7oC ![]() 1n7qC ![]() 1n7rC ![]() 1lohS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 82154.469 Da / Num. of mol.: 1 / Mutation: W292A/F343V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.93 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→50 Å / Num. obs: 127182 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.062 / Rsym value: 0.062 |
Reflection shell | Resolution: 1.55→1.61 Å / Rmerge(I) obs: 0.67 / Rsym value: 0.67 / % possible all: 98.5 |
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 127336 / Num. measured all: 723619 |
Reflection shell | *PLUS % possible obs: 98.5 % / Rmerge(I) obs: 0.67 |
-
Processing
Software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1LOH Resolution: 1.55→20 Å / σ(F): 0 / σ(I): 0
| ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
| ||||||||||||||||
LS refinement shell | Resolution: 1.55→1.61 Å / Rfactor Rfree: 0.351 / Rfactor Rwork: 0.105 | ||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||
LS refinement shell | *PLUS Rfactor Rwork: 0.305 |