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Yorodumi- PDB-7dva: Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7dva | |||||||||
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Title | Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc | |||||||||
Components | Beta-N-acetylhexosaminidaseHexosaminidase | |||||||||
Keywords | HYDROLASE / GH20 / Complex | |||||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / lysosome / carbohydrate metabolic process / membrane Similarity search - Function | |||||||||
Biological species | Bacteroides thetaiotaomicron (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | |||||||||
Authors | Zhang, Z. / He, Y. / Jin, Y. | |||||||||
Funding support | United Kingdom, China, 2items
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Citation | Journal: Acs Catalysis / Year: 2023 Title: Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases Authors: Zhang, Z. / Dong, M. / Zallot, R. / Blackburn, G.M. / Wang, N. / Wang, C. / Chen, L. / Baumann, P. / Wu, Z. / Wang, Z. / Fan, H. / Roth, C. / Jin, Y. / He, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7dva.cif.gz | 424.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7dva.ent.gz | 336.8 KB | Display | PDB format |
PDBx/mmJSON format | 7dva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/7dva ftp://data.pdbj.org/pub/pdb/validation_reports/dv/7dva | HTTPS FTP |
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-Related structure data
Related structure data | 7dupC 7dvbC 8balC 8bblC 8bdpC 3rcnS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 61751.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Production host: Escherichia coli (E. coli) References: UniProt: A0A0P0FIE8, beta-N-acetylhexosaminidase #2: Sugar | #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | 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: 2.13 Å3/Da / Density % sol: 42.26 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, sitting drop Details: 10 mM of 4MU-6S-GlcNAc with 10 mg/mL protein in the buffer of 25 mM PH 8.0, =300 mM NaCl was mixed with 0.1 M BICINE, pH 8.5, 20 % (w/v) PEG 10000 at 1:1 to carry on co-crystallization. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979191 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→70.19 Å / Num. obs: 145268 / % possible obs: 97.4 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 1.55→1.58 Å / Rmerge(I) obs: 1.005 / Mean I/σ(I) obs: 2 / Num. unique obs: 7086 / CC1/2: 0.584 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3rcn Resolution: 1.55→50.483 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.147 / SU B: 3.681 / SU ML: 0.057 / Average fsc free: 0.9221 / Average fsc work: 0.9352 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.076 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.979 Å2
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Refinement step | Cycle: LAST / Resolution: 1.55→50.483 Å
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Refine LS restraints |
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LS refinement shell |
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