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- PDB-6fwl: Structure of an E333Q variant of the GH99 endo-alpha-mannanase fr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6fwl | ||||||||||||||||||||||||
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Title | Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex alpha-Glc-1,3-(1,2-anhydro-carba-mannose) | ||||||||||||||||||||||||
![]() | 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 | ![]() ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 189.1 KB | Display | ![]() |
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PDB format | ![]() | 149 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.6 KB | Display | ![]() |
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Full document | ![]() | 476.8 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 30.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fwgC ![]() 6fwiC ![]() 6fwjC ![]() 6fwmC ![]() 6fwoC ![]() 6fwpC ![]() 6fwqC ![]() 5m17S C: citing same article ( S: Starting model for refinement |
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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 |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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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: pET21a (+) / Production host: ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-BO0 / ( | #4: Sugar | ChemComp-GLC / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.28 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 3 M sodium acetate, pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→76.53 Å / Num. obs: 149038 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 1.387 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 7376 / CC1/2: 0.45 / Rpim(I) all: 0.834 / Rrim(I) all: 1.528 / % possible all: 99.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5M17 Resolution: 1.12→76.53 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.983 / SU B: 1.044 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.027 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.07 Å2
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Refinement step | Cycle: 1 / Resolution: 1.12→76.53 Å
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Refine LS restraints |
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