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Yorodumi- PDB-6yyi: Crystal structure of beta-D-xylosidase from Dictyoglomus thermoph... -
+Open data
-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 | ||||||
Components | Beta-xylosidaseXylan 1,4-b-xylosidase | ||||||
Keywords | HYDROLASE / Carbohydrate Substrate complex | ||||||
Function / homology | Function and homology information xylan 1,4-beta-xylosidase / xylan 1,4-beta-xylosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Dictyoglomus thermophilum H-6-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.67 Å | ||||||
Authors | Lafite, P. / Daniellou, R. / Bretagne, D. | ||||||
Citation | Journal: Biochimie / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yyi.cif.gz | 219.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yyi.ent.gz | 174.4 KB | Display | PDB format |
PDBx/mmJSON format | 6yyi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yy/6yyi ftp://data.pdbj.org/pub/pdb/validation_reports/yy/6yyi | HTTPS FTP |
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-Related structure data
Related structure data | 6yyhC 1px8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 61206.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dictyoglomus thermophilum H-6-12 (bacteria) Gene: DICTH_1792 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: B5YB78, xylan 1,4-beta-xylosidase #5: Sugar | ChemComp-XYP / | |
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-Non-polymers , 5 types, 92 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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