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- PDB-8tcs: Structure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyran... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tcs | ||||||
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Title | Structure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1 | ||||||
![]() | Xylose isomerase-like TIM barrel domain-containing protein | ||||||
![]() | ISOMERASE / Sugar Phosphate Isomerase | ||||||
Function / homology | Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / trehalose / ACETATE ION / : / Xylose isomerase-like TIM barrel domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: An alternative broad-specificity pathway for glycan breakdown in bacteria. Authors: Nasseri, S.A. / Lazarski, A.C. / Lemmer, I.L. / Zhang, C.Y. / Brencher, E. / Chen, H.M. / Sim, L. / Panwar, D. / Betschart, L. / Worrall, L.J. / Brumer, H. / Strynadka, N.C.J. / Withers, S.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.8 KB | Display | ![]() |
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PDB format | ![]() | 196.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8tcdC ![]() 8tcrC ![]() 8tctC ![]() 8tdaC ![]() 8tdeC ![]() 8tdfC ![]() 8tdhC ![]() 8tdiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 30761.924 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose #3: Chemical | ChemComp-CO / #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.44 M Ammonium Chloride 21% PEG 6000 0.1 M Sodium Acetate pH 5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→48.11 Å / Num. obs: 186241 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.043 / Rrim(I) all: 0.079 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.327 / Num. unique obs: 18379 / CC1/2: 0.543 / Rpim(I) all: 0.844 / Rrim(I) all: 1.578 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→44.335 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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