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Open data
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Basic information
Entry | Database: PDB / ID: 5t9a | ||||||
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Title | Crystal structure of BuGH2Cwt | ||||||
![]() | Glycoside Hydrolase | ||||||
![]() | HYDROLASE / (alpha/beta)6 barrel / glycoside hydrolase | ||||||
Function / homology | ![]() carbohydrate catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Pluvinage, B. / Boraston, A.B. / Abbott, W.D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 656.8 KB | Display | ![]() |
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PDB format | ![]() | 530.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5t98C ![]() 5t99C ![]() 5t9gC ![]() 5t9xC ![]() 5ta0C ![]() 5ta1C ![]() 5ta5C ![]() 5ta7C ![]() 5ta9C ![]() 4cu6S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 96870.695 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.73 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M magnesium sulfate, 0.1 M Tris-HCl, 20 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→117.64 Å / Num. obs: 137926 / % possible obs: 97.8 % / Redundancy: 2.2 % / CC1/2: 0.935 / Rmerge(I) obs: 0.121 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.548 / CC1/2: 0.298 / % possible all: 97.1 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4CU6 Resolution: 2.5→117.64 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.864 / SU B: 12.359 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.887 / ESU R Free: 0.33 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: 83.36 Å2 / Biso mean: 30.07 Å2 / Biso min: 4.38 Å2
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Refinement step | Cycle: final / Resolution: 2.5→117.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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