[English] 日本語
Yorodumi- PDB-8tcs: Structure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8tcs | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of trehalose bound Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1 | ||||||
Components | Xylose isomerase-like TIM barrel domain-containing protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Alistipes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Lazarski, A.C. / Worrall, L.J. / Strynadka, N.C.J. | ||||||
Funding support | Canada, 1items
| ||||||
Citation | Journal: Nature / Year: 2024 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tcs.cif.gz | 253.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tcs.ent.gz | 196.7 KB | Display | PDB format |
PDBx/mmJSON format | 8tcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tcs_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8tcs_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 8tcs_validation.xml.gz | 48.7 KB | Display | |
Data in CIF | 8tcs_validation.cif.gz | 71.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tc/8tcs ftp://data.pdbj.org/pub/pdb/validation_reports/tc/8tcs | HTTPS FTP |
-Related structure data
Related structure data | 8tcdC 8tcrC 8tctC 8tdaC 8tdeC 8tdfC 8tdhC 8tdiC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30761.924 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Alistipes (bacteria) / Gene: BN590_01572 / Production host: Escherichia coli (E. coli) / References: UniProt: R6XSE3 #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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.35 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→44.335 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.175 / SU B: 1.661 / SU ML: 0.059 / Average fsc free: 0.9608 / Average fsc work: 0.9691 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.073 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→44.335 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|