+Open data
-Basic information
Entry | Database: PDB / ID: 5mqr | |||||||||||||||
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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 / SAD / Resolution: 2.2 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 | 5mqr.cif.gz | 459.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqr.ent.gz | 386.4 KB | Display | PDB format |
PDBx/mmJSON format | 5mqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mqr_validation.pdf.gz | 465.5 KB | Display | wwPDB validaton report |
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Full document | 5mqr_full_validation.pdf.gz | 468.5 KB | Display | |
Data in XML | 5mqr_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 5mqr_validation.cif.gz | 71.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqr ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqr | HTTPS FTP |
-Related structure data
Related structure data | 5mqmC 5mqnC 5mqoC 5mqsC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 129221.969 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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-Non-polymers , 6 types, 899 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.02 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 14% (v/v) ethylene glycol, 14% (w/v) PEG 8000, 30 mM of each di-, tri, tetra- and penta-ethylene glycol, 50 mM hepes and 50 mM MOPS pH 7.5 |
-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: 2.2→49.25 Å / Num. obs: 90935 / % possible obs: 99.3 % / Observed criterion σ(I): 1.5 / Redundancy: 6.6 % / CC1/2: 0.993 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.495 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→49.25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.739 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.147 / 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: 30.308 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→49.25 Å
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Refine LS restraints |
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