+Open data
-Basic information
Entry | Database: PDB / ID: 6je8 | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of a beta-N-acetylhexosaminidase | ||||||
Components | Beta-N-acetylhexosaminidase | ||||||
Keywords | HYDROLASE / Catalyze / acetamidodeoxyhexohydrolase | ||||||
Function / homology | Function and homology information chitobiose catabolic process / beta-N-acetylgalactosaminidase activity / glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / lysosome / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Akkermansia muciniphila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.798 Å | ||||||
Authors | Chen, X. / Wang, J.C. / Liu, M.J. / Yang, W.Y. / Wang, Y.Z. / Tang, R.P. / Zhang, M. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Crystallographic evidence for substrate-assisted catalysis of beta-N-acetylhexosaminidas from Akkermansia muciniphila. Authors: Chen, X. / Wang, J. / Liu, M. / Yang, W. / Wang, Y. / Tang, R. / Zhang, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6je8.cif.gz | 128.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6je8.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 6je8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6je8_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6je8_full_validation.pdf.gz | 446.5 KB | Display | |
Data in XML | 6je8_validation.xml.gz | 25 KB | Display | |
Data in CIF | 6je8_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/6je8 ftp://data.pdbj.org/pub/pdb/validation_reports/je/6je8 | HTTPS FTP |
-Related structure data
Related structure data | 6jeaC 6jebC 3rcnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 53628.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Akkermansia muciniphila (strain ATCC BAA-835 / Muc) (bacteria) Strain: ATCC BAA-835 / Muc / Gene: Amuc_2018 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: B2UP57, beta-N-acetylhexosaminidase | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-FMT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.26 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 1.1M Sodium malonate, pH 7.0; 0.1 M HEPES pH 7.0; 0.5%v/v Jeffamine ED-2001 pH 7.0 and 0.2 M sodium formate; 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 19, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. obs: 50339 / % possible obs: 98.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.045 / Rrim(I) all: 0.113 / Χ2: 0.917 / Net I/σ(I): 11.7 / Num. measured all: 303267 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RCN Resolution: 1.798→46.224 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.66 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.22 Å2 / Biso mean: 19.8126 Å2 / Biso min: 4.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.798→46.224 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
|