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- PDB-8u9f: Crystal structure of Bacteroides thetaiotamicron BT1285 in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8u9f | ||||||
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Title | Crystal structure of Bacteroides thetaiotamicron BT1285 in complex with NaI | ||||||
![]() | Endo-beta-N-acetylglucosaminidase | ||||||
![]() | HYDROLASE / Endoglycosidase / ENGase / GH18 family / Bacteroides thetaiotaomicron / I-SAD | ||||||
Function / homology | ![]() mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sastre, D.E. / Navarro, M.V.A.S. / Sundberg, E.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Human gut microbes express functionally distinct endoglycosidases to metabolize the same N-glycan substrate. Authors: Sastre, D.E. / Sultana, N. / V A S Navarro, M. / Huliciak, M. / Du, J. / Cifuente, J.O. / Flowers, M. / Liu, X. / Lollar, P. / Trastoy, B. / Guerin, M.E. / Sundberg, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.3 KB | Display | ![]() |
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PDB format | ![]() | 149.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 11.8 MB | Display | ![]() |
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Full document | ![]() | 11.5 MB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 26.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8u46C ![]() 8u47C ![]() 8u48C ![]() 8w01C ![]() 8w04C 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: 30455.592 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_1285 / Production host: ![]() ![]() | ||||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-IOD / #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.81 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop Details: 0.056 M Sodium phosphate monobasic monohydrate, 1.344 M Potassium phosphate dibasic, pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97718 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→41.5 Å / Num. obs: 191890 / % possible obs: 90.8 % / Redundancy: 3 % / CC1/2: 0.997 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.08→1.14 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 17229 / CC1/2: 0.921 / % possible all: 50.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.08→41.5 Å
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Refine LS restraints |
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LS refinement shell |
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