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- PDB-6yyi: Crystal structure of beta-D-xylosidase from Dictyoglomus thermoph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6yyi | ||||||
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Title | Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose | ||||||
![]() | Beta-xylosidase | ||||||
![]() | HYDROLASE / Carbohydrate Substrate complex | ||||||
Function / homology | ![]() xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Lafite, P. / Daniellou, R. / Bretagne, D. | ||||||
![]() | ![]() Title: Crystal structure of Dictyoglomus thermophilum beta-d-xylosidase DtXyl unravels the structural determinants for efficient notoginsenoside R1 hydrolysis. Authors: Bretagne, D. / Paris, A. / de Vaumas, R. / Lafite, P. / Daniellou, 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 | ![]() | 219.8 KB | Display | ![]() |
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PDB format | ![]() | 174.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 903.6 KB | Display | ![]() |
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Full document | ![]() | 914.1 KB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6yyhC ![]() 1px8S 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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1 |
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Unit cell |
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Components
-Protein / Sugars , 2 types, 3 molecules AB![](data/chem/img/XYP.gif)
![](data/chem/img/XYP.gif)
#1: Protein | Mass: 61206.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: DICTH_1792 / Plasmid: pET28a / Production host: ![]() ![]() #5: Sugar | ChemComp-XYP / | |
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-Non-polymers , 5 types, 92 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CIT / | #4: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Ammonium sulfate 10% PEG 4000 0,1M Sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2020 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.67→48.57 Å / Num. obs: 43883 / % possible obs: 99.8 % / Redundancy: 20.765 % / Biso Wilson estimate: 53.801 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.176 / Χ2: 0.835 / Net I/σ(I): 17.17 / Num. measured all: 911219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PX8 Resolution: 2.67→48.57 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.68 Å2 / Biso mean: 53.4438 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.67→48.57 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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