+Open data
-Basic information
Entry | Database: PDB / ID: 5muj | |||||||||||||||
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Title | BT0996 RGII Chain B Complex | |||||||||||||||
Components | Beta-galactosidase | |||||||||||||||
Keywords | HYDROLASE / glycoside hydrolase / arabinofuranosidase / plant pectin / RGII | |||||||||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.37 Å | |||||||||||||||
Authors | Cartmell, A. / Basle, A. / Ndeh, D. / Luis, A.S. / Venditto, I. / Labourel, A. / Rogowski, 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 | 5muj.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5muj.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 5muj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5muj_validation.pdf.gz | 861.8 KB | Display | wwPDB validaton report |
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Full document | 5muj_full_validation.pdf.gz | 865.9 KB | Display | |
Data in XML | 5muj_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 5muj_validation.cif.gz | 29.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mu/5muj ftp://data.pdbj.org/pub/pdb/validation_reports/mu/5muj | HTTPS FTP |
-Related structure data
Related structure data | 5mqmC 5mqnC 5mqoC 5mqrC 5mqsC 5msxC 5msyC 5mt2C 5muiC 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: 44148.199 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Gene: BT_0996 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A921 |
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#2: Polysaccharide | alpha-L-rhamnopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-3)]alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)- ...alpha-L-rhamnopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-3)]alpha-L-arabinopyranose-(1-4)-[4-O-[(1R)-1-hydroxyethyl]-2-O-methyl-alpha-L-fucopyranose-(1-2)]beta-D-galactopyranose-(1-2)-alpha-D-aceric acid-(1-4)-alpha-L-rhamnopyranose-(1-3)-3-C-(hydroxylmethyl)-alpha-D-erythrofuranose Type: oligosaccharide / Mass: 1247.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.09 Å3/Da / Density % sol: 41.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350 and 0.2 M Lithium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→44.85 Å / Num. obs: 74740 / % possible obs: 99 % / Redundancy: 3.6 % / Net I/σ(I): 1.4 |
-Processing
Software |
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Refinement | Resolution: 1.37→44.85 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.929 / SU B: 5.596 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.075 / 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: 16.851 Å2
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Refinement step | Cycle: 1 / Resolution: 1.37→44.85 Å
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Refine LS restraints |
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