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Yorodumi- PDB-6fwj: Structure of the GH99 endo-alpha-mannanase from Bacteroides xylan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fwj | ||||||||||||||||||||||||
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Title | Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-mannosamine) and alpha-1,2-mannobiose | ||||||||||||||||||||||||
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: 1.04 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
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fwj.cif.gz | 189.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fwj.ent.gz | 148.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/6fwj ftp://data.pdbj.org/pub/pdb/validation_reports/fw/6fwj | HTTPS FTP |
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-Related structure data
Related structure data | 6fwgC 6fwiC 6fwlC 6fwmC 6fwoC 6fwpC 6fwqC 5m17S C: citing same article (ref.) S: Starting model for refinement |
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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 |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43933.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides xylanisolvens XB1A (bacteria) Gene: BXY_34140 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D6D1V7 |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose / 2alpha-alpha-mannobiose |
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#5: Sugar | ChemComp-GLC / |
-Non-polymers , 3 types, 383 molecules
#3: Chemical | ChemComp-ACT / |
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#4: Chemical | ChemComp-E9K / ( |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.85 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 3 M sodium acetate, pH 6.4 - 7.4 / PH range: 6.4 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 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: 1.04→76.82 Å / Num. obs: 185423 / % possible obs: 98.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 12.71 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.042 / Rrim(I) all: 0.081 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.04→1.06 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.346 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7436 / CC1/2: 0.455 / Rpim(I) all: 0.601 / Rrim(I) all: 1.482 / % possible all: 80.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5M17 Resolution: 1.04→76.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.708 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.021 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.751 Å2
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Refinement step | Cycle: 1 / Resolution: 1.04→76.82 Å
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Refine LS restraints |
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