+Open data
-Basic information
Entry | Database: PDB / ID: 5ta7 | ||||||
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Title | Crystal structure of BuGH117Bwt | ||||||
Components | Glycoside Hydrolase | ||||||
Keywords | HYDROLASE / agarase / glycoside hydrolase | ||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Bacteroides uniformis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å | ||||||
Authors | Pluvinage, B. / Boraston, A.B. | ||||||
Citation | Journal: Nat Commun / Year: 2018 Title: Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont. Authors: Pluvinage, B. / Grondin, J.M. / Amundsen, C. / Klassen, L. / Moote, P.E. / Xiao, Y. / Thomas, D. / Pudlo, N.A. / Anele, A. / Martens, E.C. / Inglis, G.D. / Uwiera, R.E.R. / Boraston, A.B. / Abbott, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ta7.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ta7.ent.gz | 135.3 KB | Display | PDB format |
PDBx/mmJSON format | 5ta7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/5ta7 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/5ta7 | HTTPS FTP |
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-Related structure data
Related structure data | 5t98C 5t99C 5t9aC 5t9gC 5t9xC 5ta0C 5ta1C 5ta5C 5ta9C 4ak5S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 45636.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: NP1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D0TCD6*PLUS #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | #5: 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: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1-0.18M LiSo4, 0.1M Tris-HCl, 25-30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: May 4, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→90 Å / Num. obs: 40335 / % possible obs: 99.6 % / Redundancy: 7.1 % / CC1/2: 0.993 / Rmerge(I) obs: 0.147 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 4.2 / CC1/2: 0.886 / % possible all: 98.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4AK5 Resolution: 2.35→74.91 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.807 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.291 / ESU R Free: 0.203 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.14 Å2 / Biso mean: 18.445 Å2 / Biso min: 2.46 Å2
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Refinement step | Cycle: final / Resolution: 2.35→74.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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