[English] 日本語
![](img/lk-miru.gif)
- PDB-6s0e: Crystal structure of an inverting family GH156 exosialidase from ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6s0e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with N-Acetyl-2,3-dehydro-2-deoxyneuraminic acid | ||||||
![]() | exosialidase from uncultured bacterium pG7 | ||||||
![]() | HYDROLASE / (beta/alpha )8 barrel / sialidase / inverting / homodimer | ||||||
Function / homology | ACETATE ION / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bule, P. / Blagova, E. / Chuzel, L. / Taron, C.H. / Davies, G.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action. Authors: Bule, P. / Chuzel, L. / Blagova, E. / Wu, L. / Gray, M.A. / Henrissat, B. / Rapp, E. / Bertozzi, C.R. / Taron, C.H. / Davies, G.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 413 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 340 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 42.2 KB | Display | |
Data in CIF | ![]() | 61.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rzdSC ![]() 6s00C ![]() 6s04C ![]() 6s0fC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein / Sugars , 2 types, 4 molecules AB![](data/chem/img/DAN.gif)
![](data/chem/img/DAN.gif)
#1: Protein | Mass: 58786.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET29a / Production host: ![]() ![]() #5: Sugar | |
---|
-Non-polymers , 5 types, 505 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-PG4 / | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.2 M potassium bromide, 15% PEG 4000, 0.1 M sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 21, 2018 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9159 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→78.76 Å / Num. obs: 87227 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.91 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.099 / Rrim(I) all: 0.198 / Net I/σ(I): 5 / Num. measured all: 345513 / Scaling rejects: 2353 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6RZD Resolution: 1.9→64.58 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.845 / SU B: 13.302 / SU ML: 0.198 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 52.69 Å2 / Biso mean: 20.945 Å2 / Biso min: 0.51 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→64.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | T23: -0.0024 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|