[English] 日本語
![](img/lk-miru.gif)
- PDB-6fwq: Structure of an E333Q variant of the GH99 endo-alpha-mannanase fr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6fwq | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-1,3-mannobiose and alpha-1,2-mannobiose | ||||||||||||||||||||||||
![]() | Glycosyl hydrolase family 71 | ||||||||||||||||||||||||
![]() | HYDROLASE | ||||||||||||||||||||||||
Function / homology | ![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. ...Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Lu, D. / Sollogoub, M. / Rovira, C. / Jimenez-Barbero, J. / Davies, G.J. / Williams, S.J. | ||||||||||||||||||||||||
Funding support | ![]() ![]() ![]()
| ||||||||||||||||||||||||
![]() | ![]() Title: An Epoxide Intermediate in Glycosidase Catalysis. Authors: Sobala, L.F. / Speciale, G. / Zhu, S. / Raich, L. / Sannikova, N. / Thompson, A.J. / Hakki, Z. / Lu, D. / Shamsi Kazem Abadi, S. / Lewis, A.R. / Rojas-Cervellera, V. / Bernardo-Seisdedos, G. ...Authors: Sobala, L.F. / Speciale, G. / Zhu, S. / Raich, L. / Sannikova, N. / Thompson, A.J. / Hakki, Z. / Lu, D. / Shamsi Kazem Abadi, S. / Lewis, A.R. / Rojas-Cervellera, V. / Bernardo-Seisdedos, G. / Zhang, Y. / Millet, O. / Jimenez-Barbero, J. / Bennet, A.J. / Sollogoub, M. / Rovira, C. / Davies, G.J. / Williams, S.J. #1: ![]() Title: An Epoxide Intermediate in Glycosidase Catalysis Authors: Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Lu, D. / ...Authors: Sobala, L.F. / Speciale, G. / Hakki, Z. / Fernandes, P.Z. / Raich, L. / Rojas-Cervellera, V. / Bennet, A. / Thompson, A.J. / Bernardo-Seisdedos, G. / Millet, O. / Zhu, S. / Lu, D. / Sollogoub, M. / Rovira, C. / Jimenez-Barbero, J. / Davies, G.J. / Williams, S.J. | ||||||||||||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 172.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 134.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 22.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fwgC ![]() 6fwiC ![]() 6fwjC ![]() 6fwlC ![]() 6fwmC ![]() 6fwoC ![]() 6fwpC ![]() 5m17S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: ![]() Details: Diffraction images used to solve the structures published in the article "An Epoxide Intermediate in Glycosidase Catalysis" Metadata reference: 10.5281/zenodo.4424526 |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 43932.609 Da / Num. of mol.: 1 / Mutation: E333Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BXY_34140 / Plasmid: pET28a (+) / Production host: ![]() ![]() |
---|---|
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose / 3alpha-alpha-mannobiose |
#3: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose |
#4: Chemical | ChemComp-NA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.78 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 3 M sodium acetate, pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→76.83 Å / Num. obs: 47947 / % possible obs: 99.6 % / Redundancy: 4 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.014 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2336 / CC1/2: 0.406 / Rpim(I) all: 0.578 / Rrim(I) all: 1.171 / % possible all: 99.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5M17 Resolution: 1.65→76.83 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.29 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.084 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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: 26.855 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.65→76.83 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|