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- PDB-6t8i: Crystal structure of wild type EndoBT-3987 from Bacteroides theta... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6t8i | ||||||
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Title | Crystal structure of wild type EndoBT-3987 from Bacteroides thetaiotamicron VPI-5482 | ||||||
![]() | Endo-beta-N-acetylglucosaminidase F1 | ||||||
![]() | HYDROLASE / endo-b-N-acetylglucosaminidase / EndoBT / glycoside hydrolase | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Trastoy, B. / Du, J.J. / Klontz, E.H. / Cifuente, J.O. / Sundberg, E.J. / Guerin, M.E. | ||||||
![]() | ![]() Title: Structural basis of mammalian high-mannose N-glycan processing by human gut Bacteroides. Authors: Trastoy, B. / Du, J.J. / Klontz, E.H. / Li, C. / Cifuente, J.O. / Wang, L.X. / Sundberg, E.J. / Guerin, M.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 263 KB | Display | ![]() |
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PDB format | ![]() | 216.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 428.6 KB | Display | ![]() |
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Full document | ![]() | 428.5 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6t8kC ![]() 6t8lC ![]() 6tcvC ![]() 6tcwC ![]() 3pohS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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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: 49193.746 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3987 / Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 200 mM sodium bromide, and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→58.143 Å / Num. obs: 85242 / % possible obs: 100 % / Redundancy: 9.8 % / CC1/2: 1 / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.4→1.45 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 8417 / CC1/2: 0.942 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3POH Resolution: 1.4→58.143 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.85 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.79 Å2 / Biso mean: 25.6811 Å2 / Biso min: 10.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→58.143 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: 57.1832 Å / Origin y: 19.8188 Å / Origin z: 63.9391 Å
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Refinement TLS group |
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