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- PDB-8tcd: Structure of Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1 -
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Open data
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Basic information
Entry | Database: PDB / ID: 8tcd | ||||||
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Title | Structure of Alistipes sp. 3-Keto-beta-glucopyranoside-1,2-Lyase AL1 | ||||||
![]() | Sugar phosphate isomerase | ||||||
![]() | ISOMERASE / Sugar Phosphate Isomerase | ||||||
Function / homology | ACETATE ION / : / : ![]() | ||||||
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 | ![]() | 236.4 KB | Display | ![]() |
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PDB format | ![]() | 187 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.4 KB | Display | ![]() |
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Full document | ![]() | 479.4 KB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 62.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8tcrC ![]() 8tcsC ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 32738.215 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-CO / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.27 M Ammonium Chloride 17% 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 PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→47.57 Å / Num. obs: 89795 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.07 / Rrim(I) all: 0.177 / Χ2: 1.03 / Net I/σ(I): 9.7 / Num. measured all: 577872 |
Reflection shell | Resolution: 1.9→1.93 Å / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 1.954 / Num. measured all: 26884 / Num. unique obs: 4511 / CC1/2: 0.507 / Rpim(I) all: 0.876 / Rrim(I) all: 2.145 / Χ2: 1.24 / Net I/σ(I) obs: 1.1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 22.987 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→46.39 Å
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Refine LS restraints |
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