+Open data
-Basic information
Entry | Database: PDB / ID: 5ta5 | |||||||||
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Title | Crystal structure of BuGH86wt in complex with neoagarooctaose | |||||||||
Components | Glycoside Hydrolase | |||||||||
Keywords | HYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bacteroides uniformis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 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 | 5ta5.cif.gz | 301.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ta5.ent.gz | 239.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ta5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ta5_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5ta5_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5ta5_validation.xml.gz | 65.3 KB | Display | |
Data in CIF | 5ta5_validation.cif.gz | 93 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ta/5ta5 ftp://data.pdbj.org/pub/pdb/validation_reports/ta/5ta5 | HTTPS FTP |
-Related structure data
Related structure data | 5t98C 5t99C 5t9aC 5t9gC 5t9xC 5ta0C 5ta1C 5ta7C 5ta9C 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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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 74748.672 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: A0A2D0TCD3*PLUS |
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-Sugars , 2 types, 2 molecules
#2: Polysaccharide | 3,6-anhydro-alpha-L-galactopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-galactopyranose-(1-4)-3,6-anhydro-alpha-L-galactopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 1178 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 2.36 Å3/Da / Density % sol: 47.89 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.2M ammonium sulfate, 0.1M Bis-Tris, 21% PEG 3350 |
-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: Jul 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: 1.65→83.08 Å / Num. obs: 159705 / % possible obs: 97.1 % / Redundancy: 4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.141 / Mean I/σ(I) obs: 7.8 / CC1/2: 0.98 / % possible all: 94.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→83.08 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.248 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.52 Å2 / Biso mean: 12.767 Å2 / Biso min: 4.64 Å2
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Refinement step | Cycle: final / Resolution: 1.65→83.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
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