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Yorodumi- PDB-7cbn: Crystal structure of beta-N-acetylhexosaminidase Am0868 from Akke... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cbn | ||||||
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Title | Crystal structure of beta-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila | ||||||
Components | Beta-N-acetylhexosaminidaseHexosaminidase | ||||||
Keywords | HYDROLASE / Akkermansia muciniphila / beta-N-acetylhexosaminidases / Mucin degradation | ||||||
Function / homology | Function and homology information beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / polysaccharide catabolic process Similarity search - Function | ||||||
Biological species | Akkermansia muciniphila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Xu, W. / Wang, M. / Zhang, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2020 Title: Structural and biochemical analyses of beta-N-acetylhexosaminidase Am0868 from Akkermansia muciniphila involved in mucin degradation. Authors: Xu, W. / Yang, W. / Wang, Y. / Wang, M. / Zhang, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cbn.cif.gz | 140.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cbn.ent.gz | 104.7 KB | Display | PDB format |
PDBx/mmJSON format | 7cbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/7cbn ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cbn | HTTPS FTP |
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-Related structure data
Related structure data | 7cboC 6q63S 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
#1: Protein | Mass: 61135.008 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_0868 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2UQG6, beta-N-acetylhexosaminidase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.76 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.24 M sodium malonate pH 7.0 and 20% Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→50 Å / Num. obs: 61817 / % possible obs: 99.9 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.027 / Rrim(I) all: 0.094 / Χ2: 0.978 / Net I/σ(I): 9.3 / Num. measured all: 734909 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q63 Resolution: 1.7→38.777 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.46 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.1 Å2 / Biso mean: 24.3724 Å2 / Biso min: 10.65 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→38.777 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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