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Open data
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Basic information
Entry | Database: PDB / ID: 5t99 | ||||||
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Title | Crystal structure of BuGH2Awt in complex with Galactoisofagomine | ||||||
![]() | 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. | ||||||
![]() | ![]() 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 | ![]() | 328.6 KB | Display | ![]() |
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PDB format | ![]() | 261.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 472.9 KB | Display | ![]() |
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Full document | ![]() | 476.1 KB | Display | |
Data in XML | ![]() | 57.8 KB | Display | |
Data in CIF | ![]() | 85.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5t98C ![]() 5t9aC ![]() 5t9gC ![]() 5t9xC ![]() 5ta0C ![]() 5ta1C ![]() 5ta5C ![]() 5ta7C ![]() 5ta9C C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 93413.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M ammonium citrate dibasic, 20-22% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9753 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→92.82 Å / Num. obs: 81323 / % possible obs: 100 % / Redundancy: 8.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.188 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.787 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.759 / % possible all: 99.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() 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: 92.35 Å2 / Biso mean: 26.999 Å2 / Biso min: 4.74 Å2
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Refinement step | Cycle: final / Resolution: 2.4→92.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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