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Open data
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Basic information
Entry | Database: PDB / ID: 8dhl | |||||||||
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Title | Tannerella forsythia beta-glucuronidase (L2) | |||||||||
![]() | Glycosyl hydrolase family 2, sugar binding domain protein | |||||||||
![]() | HYDROLASE / Glycoside hydrolase family 2 / TIM barrel domain | |||||||||
Function / homology | ![]() carbohydrate catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Lietzan, A.D. / Redinbo, M.R. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Microbial beta-glucuronidases drive human periodontal disease etiology. Authors: Lietzan, A.D. / Simpson, J.B. / Walton, W.G. / Jariwala, P.B. / Xu, Y. / Boynton, M.H. / Liu, J. / Redinbo, M.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 660.2 KB | Display | ![]() |
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PDB format | ![]() | 538.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dheC ![]() 8dhvC ![]() 8dhwC ![]() 8e72C ![]() 5uj6S S: Starting model for refinement 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: 100769.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CA / #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: 2.42 Å3/Da / Density % sol: 49.18 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 6% (w/v) PEG8000, 8% (v/v) ethylene glycol, 2% (v/v) glycerol, 0.1 M Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 4, 2019 | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.96802 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→103.66 Å / Num. obs: 87551 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 22.19 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.193 / Rpim(I) all: 0.081 / Rrim(I) all: 0.21 / Net I/σ(I): 7 / Num. measured all: 575179 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5UJ6 Resolution: 2.3→78.77 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.27 / 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: 71.66 Å2 / Biso mean: 22.2024 Å2 / Biso min: 9.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→78.77 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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