[English] 日本語
![](img/lk-miru.gif)
- PDB-1loh: Streptococcus pneumoniae Hyaluronate Lyase in Complex with Hexasa... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1loh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Streptococcus pneumoniae Hyaluronate Lyase in Complex with Hexasaccharide Hyaluronan Substrate | |||||||||
![]() | Hyaluronate Lyase | |||||||||
![]() | LYASE / PROTEIN-CARBOHYDRATE COMPLEX | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Jedrzejas, M.J. / Mello, L.V. / De Groot, B.L. / Li, S. | |||||||||
![]() | ![]() Title: Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. Authors: Jedrzejas, M.J. / Mello, L.V. / de Groot, B.L. / Li, S. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 171.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 131.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 759.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 782.3 KB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 50.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 82301.641 Da / Num. of mol.: 1 / Mutation: Y408F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: GenBank: 437705, UniProt: Q54873*PLUS, hyaluronate lyase |
---|---|
#2: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.86 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: OXFORD / Detector: CCD / Date: Mar 20, 2001 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 60259 / Num. obs: 60259 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 99.4 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. measured all: 407437 / Rmerge(I) obs: 0.167 |
Reflection shell | *PLUS % possible obs: 99.4 % / Rmerge(I) obs: 0.91 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 50 Å / % reflection Rfree: 1 % / Rfactor Rfree: 0.243 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2 Å / Lowest resolution: 2.07 Å / Rfactor Rfree: 0.384 / Rfactor Rwork: 0.324 |