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Open data
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Basic information
Entry | Database: PDB / ID: 8tdi | ||||||
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Title | Structure of P2B11 Glucuronide-3-dehydrogenase | ||||||
![]() | P2B11 Glucuronide-3-dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Dehydrogenase | ||||||
Function / homology | NICOTINAMIDE-ADENINE-DINUCLEOTIDE![]() | ||||||
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 | ![]() | 885.5 KB | Display | ![]() |
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PDB format | ![]() | 739.7 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 ![]() 8tcsC ![]() 8tctC ![]() 8tdaC ![]() 8tdeC ![]() 8tdfC ![]() 8tdhC 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: 45297.680 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-TRS / #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: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M LiSO4 19% 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: Apr 14, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.18 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→48.37 Å / Num. obs: 161121 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.13 / Χ2: 1.02 / Net I/σ(I): 13.7 / Num. measured all: 1108051 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 1.919 / Num. measured all: 55713 / Num. unique obs: 7990 / CC1/2: 0.373 / Rpim(I) all: 0.78 / Rrim(I) all: 2.074 / Χ2: 1.02 / Net I/σ(I) obs: 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: 71.856 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→48.37 Å
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Refine LS restraints |
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