[English] 日本語
Yorodumi- PDB-6fwg: Structure of an E333Q variant of the GH99 endo-alpha-mannanase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fwg | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with tetramannoside yeast mannan fragment | ||||||||||||||||||||||||
Components | Glycosyl hydrolase family 71 | ||||||||||||||||||||||||
Keywords | HYDROLASE | ||||||||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||||||||
Biological species | Bacteroides xylanisolvens XB1A (bacteria) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å | ||||||||||||||||||||||||
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. ...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 | United Kingdom, Australia, Spain, 7items
| ||||||||||||||||||||||||
Citation | Journal: Acs Cent.Sci. / Year: 2020 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: Journal: ChemRxiv / Year: 2019 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fwg.cif.gz | 183.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fwg.ent.gz | 143.3 KB | Display | PDB format |
PDBx/mmJSON format | 6fwg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fwg_validation.pdf.gz | 785 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fwg_full_validation.pdf.gz | 787.4 KB | Display | |
Data in XML | 6fwg_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 6fwg_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/6fwg ftp://data.pdbj.org/pub/pdb/validation_reports/fw/6fwg | HTTPS FTP |
-Related structure data
Related structure data | 6fwiC 6fwjC 6fwlC 6fwmC 6fwoC 6fwpC 6fwqC 5m17S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.4424526 / Data set type: diffraction image data 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 on special symmetry positions |
|
-Components
#1: Protein | Mass: 43932.609 Da / Num. of mol.: 1 / Mutation: E333Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria) Gene: BXY_34140 / Plasmid: pET-28a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6D1V7 | ||
---|---|---|---|
#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-methyl alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranoside Source method: isolated from a genetically manipulated source | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.07 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 3M sodium acetate, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.07→76.28 Å / Num. obs: 170023 / % possible obs: 100 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.66 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.07→1.09 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1 / Num. unique obs: 8334 / CC1/2: 0.398 / Rpim(I) all: 0.705 / Rrim(I) all: 1.692 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M17 Resolution: 1.07→76.28 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.984 / SU B: 0.847 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / 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: 16.738 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.07→76.28 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|