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Open data
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Basic information
Entry | Database: PDB / ID: 8v31 | ||||||
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Title | Structure of Alistipes sp. 3-Keto-2-hydroxy-glucal-hydratase AL2 | ||||||
![]() | Glycosyl hydrolase | ||||||
![]() | HYDROLASE / Hydratase / GH16-like | ||||||
Function / homology | 3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Prokaryotic membrane lipoprotein lipid attachment site profile. / hydrolase activity / Glycosyl hydrolase![]() | ||||||
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. / 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 | ![]() | 117.6 KB | Display | ![]() |
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PDB format | ![]() | 87 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.4 KB | Display | ![]() |
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Full document | ![]() | 458.2 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 27 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 30959.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: 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: 3.36 Å3/Da / Density % sol: 63.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M Magnesium Chloride, 25% PEG 3350, 0.1 M Bis-Tris methane pH 5.5 |
-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: Jul 19, 2023 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.18085 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.65→47.54 Å / Num. obs: 24911 / % possible obs: 99.9 % / Redundancy: 18.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.047 / Rrim(I) all: 0.15 / Net I/σ(I): 22.9 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 61.222 Å2
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Refinement step | Cycle: LAST / Resolution: 2.65→47.54 Å
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Refine LS restraints |
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LS refinement shell |
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