+Open data
-Basic information
Entry | Database: PDB / ID: 5mqs | |||||||||||||||
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Title | Sialidase BT_1020 | |||||||||||||||
Components | Beta-L-arabinobiosidase | |||||||||||||||
Keywords | HYDROLASE / sialidase / arabinofuranosidase / plant pectin | |||||||||||||||
Function / homology | Function and homology information (Ara-f)3-Hyp beta-L-arabinobiosidase / hydrolase activity, acting on glycosyl bonds / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||||||||
Authors | Basle, A. / Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Venditto, I. / Labourel, A. / Gilbert, H.J. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Nature / Year: 2017 Title: Complex pectin metabolism by gut bacteria reveals novel catalytic functions. Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / ...Authors: Ndeh, D. / Rogowski, A. / Cartmell, A. / Luis, A.S. / Basle, A. / Gray, J. / Venditto, I. / Briggs, J. / Zhang, X. / Labourel, A. / Terrapon, N. / Buffetto, F. / Nepogodiev, S. / Xiao, Y. / Field, R.A. / Zhu, Y. / O'Neill, M.A. / Urbanowicz, B.R. / York, W.S. / Davies, G.J. / Abbott, D.W. / Ralet, M.C. / Martens, E.C. / Henrissat, B. / Gilbert, H.J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mqs.cif.gz | 433.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqs.ent.gz | 351.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mqs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mqs_validation.pdf.gz | 449.8 KB | Display | wwPDB validaton report |
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Full document | 5mqs_full_validation.pdf.gz | 451.4 KB | Display | |
Data in XML | 5mqs_validation.xml.gz | 35.7 KB | Display | |
Data in CIF | 5mqs_validation.cif.gz | 49.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqs ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqs | HTTPS FTP |
-Related structure data
Related structure data | 5mqmC 5mqnC 5mqoC 5mqrC 5msxC 5msyC 5mt2C 5muiC 5mujC 5mwkC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 127533.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Gene: hypBA2, Btheta7330_02635 / Plasmid: pet28b / Production host: Escherichia coli (E. coli) References: UniProt: A0A0P0FQG4, UniProt: Q8A8Z7*PLUS, (Ara-f)3-Hyp beta-L-arabinobiosidase |
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#2: Sugar | ChemComp-AHR / |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-CA / |
#5: 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: 3.57 Å3/Da / Density % sol: 65.56 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 15% (v/v) ethylene glycol, 15% (w/v) PEG 8000, 20 mM D-glucose, 20 mM D-mannose, 20 mM D- galactose, L-fucose, D-xylose, N-acetyl-D-glucosamine, 300 mM L-arabinose, 44.5 mM imidazole, 55.5 mM MES pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 3→49.29 Å / Num. all: 274267 / Num. obs: 37085 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 7.4 % / CC1/2: 0.966 / Rmerge(I) obs: 0.312 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 3→3.13 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.316 / Mean I/σ(I) obs: 1.7 / Num. unique all: 4450 / CC1/2: 0.632 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BT_1020 native Resolution: 3→49.29 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.85 / SU B: 39.866 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.4 / 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: 29.598 Å2
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Refinement step | Cycle: 1 / Resolution: 3→49.29 Å
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Refine LS restraints |
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