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Yorodumi- PDB-3nsn: Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nsn | |||||||||
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Title | Crystal Structure of insect beta-N-acetyl-D-hexosaminidase OfHex1 complexed with TMG-chitotriomycin | |||||||||
Components | N-acetylglucosaminidaseAlpha-N-acetylglucosaminidase | |||||||||
Keywords | HYDROLASE / beta-N-acetyl-D-hexosaminidase | |||||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / chitin catabolic process / polysaccharide catabolic process / beta-N-acetylglucosaminidase activity / lysosome / plasma membrane Similarity search - Function | |||||||||
Biological species | Ostrinia furnacalis (Asian corn borer) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Zhang, H. / Liu, T. / Liu, F. / Yang, Q. / Shen, X. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Structural Determinants of an Insect {beta}-N-Acetyl-D-hexosaminidase Specialized as a Chitinolytic Enzyme Authors: Liu, T. / Zhang, H. / Liu, F. / Wu, Q. / Shen, X. / Yang, Q. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nsn.cif.gz | 139.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nsn.ent.gz | 106.1 KB | Display | PDB format |
PDBx/mmJSON format | 3nsn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ns/3nsn ftp://data.pdbj.org/pub/pdb/validation_reports/ns/3nsn | HTTPS FTP |
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-Related structure data
Related structure data | 3nsmC 1o7aS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 65551.906 Da / Num. of mol.: 1 / Fragment: residues 23-594 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ostrinia furnacalis (Asian corn borer) / Production host: Pichia pastoris (fungus) / References: UniProt: Q06GJ0, beta-N-acetylhexosaminidase |
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#2: Polysaccharide | 2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...2-deoxy-2-(trimethylammonio)-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / TMG-chitotriomycin |
#3: Water | ChemComp-HOH / |
Nonpolymer details | THE LIGAND TMX IS LINKED TO CTO. IT IS CALLED AS TMG-CHITOTRIOM |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.55 Å3/Da / Density % sol: 72.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES, 200mM MgCl2, 30% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 3, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 55689 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1o7a Resolution: 2.1→28.13 Å / Cor.coef. Fo:Fc: 0.938 / SU B: 3.122 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→28.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.101→2.155 Å / Total num. of bins used: 20
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