[English] 日本語
![](img/lk-miru.gif)
- PDB-6t2r: Prominent members of the human gut microbiota express endo-acting... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6t2r | ||||||
---|---|---|---|---|---|---|---|
Title | Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown | ||||||
![]() | Beta-glycosidase | ||||||
![]() | HYDROLASE / Human gut microbiota / mucin degradation / O-glycanases / GH16 / endo beta-galactosidase | ||||||
Function / homology | licheninase activity / licheninase / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / Beta-glycosidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Crouch, L.I. / Liberato, M.V. / Ubranowicz, P.A. / Basle, A. / Lamb, C.A. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. ...Crouch, L.I. / Liberato, M.V. / Ubranowicz, P.A. / Basle, A. / Lamb, C.A. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madubic, K. / Chater, P. / Zhang, F. / Linhardt, R.J. / Spence, D.I.R. / Bolam, D.N. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. Authors: Crouch, L.I. / Liberato, M.V. / Urbanowicz, P.A. / Basle, A. / Lamb, C.A. / Stewart, C.J. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madunic, K. / Wuhrer, M. / ...Authors: Crouch, L.I. / Liberato, M.V. / Urbanowicz, P.A. / Basle, A. / Lamb, C.A. / Stewart, C.J. / Cooke, K. / Doona, M. / Needham, S. / Brady, R.R. / Berrington, J.E. / Madunic, K. / Wuhrer, M. / Chater, P. / Pearson, J.P. / Glowacki, R. / Martens, E.C. / Zhang, F. / Linhardt, R.J. / Spencer, D.I.R. / Bolam, D.N. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6t2nC ![]() 6t2oC ![]() 6t2pC ![]() 6t2qC ![]() 6t2sC ![]() 3ilnS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 30488.877 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: bglA_5, DW190_07485, DW794_15185, DWY26_17235, DWZ35_07795, DXA49_02580, EAJ00_16275, ERS852494_03890 Production host: ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.03 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 1 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→43.57 Å / Num. obs: 19202 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.995 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1554 / CC1/2: 0.743 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3ILN Resolution: 2.1→43.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.295 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.179 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.623 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→43.57 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|