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- PDB-7dup: Apo structure of wild type Bt4394, a GH20 family sulfoglycosidase -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dup | ||||||
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Title | Apo structure of wild type Bt4394, a GH20 family sulfoglycosidase | ||||||
![]() | Beta-N-acetylhexosaminidase | ||||||
![]() | HYDROLASE / GH20 / apo | ||||||
Function / homology | ![]() glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / lysosome / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Z. / He, Y. / Jin, Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 235.9 KB | Display | ![]() |
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PDB format | ![]() | 181.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.8 KB | Display | ![]() |
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Full document | ![]() | 440.1 KB | Display | |
Data in XML | ![]() | 24.3 KB | Display | |
Data in CIF | ![]() | 37.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dvaC ![]() 7dvbC ![]() 8balC ![]() 8bblC ![]() 8bdpC ![]() 3rcnS 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: 61751.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: exo I_9, Btheta7330_03706, DW780_13390, DXA83_13370, F9Z91_18555, GAN91_16275, GAO05_07480, GAO06_07340, GAO10_07310, GAO29_03665, GAO30_05795, GAO37_05915, GAO40_07835, GAO43_09530, GAO49_ ...Gene: exo I_9, Btheta7330_03706, DW780_13390, DXA83_13370, F9Z91_18555, GAN91_16275, GAO05_07480, GAO06_07340, GAO10_07310, GAO29_03665, GAO30_05795, GAO37_05915, GAO40_07835, GAO43_09530, GAO49_05915, GAO54_04845, GAO55_21770, GAO58_12095, GAO60_04205 Production host: ![]() ![]() References: UniProt: A0A0P0FIE8, beta-N-acetylhexosaminidase | ||||||
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#2: Chemical | ChemComp-MES / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.59 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / Details: PEG 10000, MES, Cl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→73.29 Å / Num. obs: 76353 / % possible obs: 99 % / Redundancy: 5.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.62→1.65 Å / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2 / Num. unique obs: 3495 / CC1/2: 0.682 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3rcn Resolution: 1.62→73.29 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.487 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.081 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: 25.006 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→73.29 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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