[English] 日本語
![](img/lk-miru.gif)
- PDB-5n6s: Thermotoga maritima family 1 Glycoside hydrolase complexed with C... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5n6s | ||||||
---|---|---|---|---|---|---|---|
Title | Thermotoga maritima family 1 Glycoside hydrolase complexed with Carba-Cyclophellitol transition state mimic | ||||||
![]() | Beta-glucosidase A | ||||||
![]() | HYDROLASE / carba-cyclophellitol / mimic | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Offen, W. / Davies, G. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Carba-cyclophellitols Are Neutral Retaining-Glucosidase Inhibitors. Authors: Beenakker, T.J.M. / Wander, D.P.A. / Offen, W.A. / Artola, M. / Raich, L. / Ferraz, M.J. / Li, K.Y. / Houben, J.H.P.M. / van Rijssel, E.R. / Hansen, T. / van der Marel, G.A. / Codee, J.D.C. ...Authors: Beenakker, T.J.M. / Wander, D.P.A. / Offen, W.A. / Artola, M. / Raich, L. / Ferraz, M.J. / Li, K.Y. / Houben, J.H.P.M. / van Rijssel, E.R. / Hansen, T. / van der Marel, G.A. / Codee, J.D.C. / Aerts, J.M.F.G. / Rovira, C. / Davies, G.J. / Overkleeft, H.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 375.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 302.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5n6tC ![]() 1od0S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53940.648 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-Non-polymers , 8 types, 437 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/8P5.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/8P5.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-IMD / | #5: Chemical | ChemComp-8P5 / #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-PGE / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.55 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 4000, calcium acetate, trimethylamine oxide, imidazole |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→72.92 Å / Num. obs: 109393 / % possible obs: 97.3 % / Redundancy: 2.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.076 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 5304 / CC1/2: 0.755 / Rpim(I) all: 0.517 / % possible all: 95.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1OD0.PDB Resolution: 2.1→72.91 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.864 / SU B: 8.893 / SU ML: 0.232 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.252 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC. THERE ARE UNMODELLED REGIONS FOR C212-213, C359-363, C372, C423-427, D233, D361-364, D425-427 and D430-432. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DATA ARE HIGHLY ANISOTROPIC. THERE ARE UNMODELLED REGIONS FOR C212-213, C359-363, C372, C423-427, D233, D361-364, D425-427 and D430-432. THE LIGAND MOLECULES IN THE PROTEIN ACTIVE SITES ARE MODELLED AS FOLLOWS: CHAIN A, IN 2 CONFORMATIONS AT OCCUPANCIES 0.6/0.4, CHAIN B, IN 1 CONFORMATION, CHAIN C, WITH THE CARBA-CYCLOPHELLITOL AND AMIDE GROUPS AT OCCUPANCY 1, AND AZIDOBUTYL GROUP AT OCCUPANCY 0.5, CHAIN D, WITH ONLY THE CARBA-CYCLOPHELLITOL AND AMIDE MOIETIES PRESENT, AT OCCUPANCY 1.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.659 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→72.91 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|