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Yorodumi- PDB-5fd0: Streptomyces plicatus N-acetyl-beta-hexosaminidase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fd0 | ||||||
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Title | Streptomyces plicatus N-acetyl-beta-hexosaminidase in complex with NAGlucal | ||||||
Components | B-N-acetylhexosaminidase | ||||||
Keywords | HYDROLASE / Family 20 glycoside hydrolase / SpHex / GH20 / NAG-glucal / hexosaminidase / glycosidase inhibitor | ||||||
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 / carbohydrate metabolic process / lysosome / membrane Similarity search - Function | ||||||
Biological species | Streptomyces plicatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Vadlamani, G. / Mark, B.L. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Chem.Commun.(Camb.) / Year: 2016 Title: N-Acetyl glycals are tight-binding and environmentally insensitive inhibitors of hexosaminidases. Authors: Santana, A.G. / Vadlamani, G. / Mark, B.L. / Withers, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fd0.cif.gz | 210.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fd0.ent.gz | 166.8 KB | Display | PDB format |
PDBx/mmJSON format | 5fd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fd0_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 5fd0_full_validation.pdf.gz | 469.5 KB | Display | |
Data in XML | 5fd0_validation.xml.gz | 26.9 KB | Display | |
Data in CIF | 5fd0_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/5fd0 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/5fd0 | HTTPS FTP |
-Related structure data
Related structure data | 5fczC 1hp4S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | monomer according to gel filtration |
-Components
#1: Protein | Mass: 56126.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces plicatus (bacteria) / Gene: hex / Plasmid: pET-3a / Details (production host): Ampicillin resistance / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: O85361 | ||||
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#2: Sugar | ChemComp-NAG / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.03 Å3/Da / Density % sol: 69.44 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.8M ammonium sulphate, 0.1M trisodium citrate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→54.81 Å / Num. obs: 61567 / % possible obs: 98.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 23.06 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 2.3 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HP4 Resolution: 2→33.759 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.28 / 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 mean: 25.41 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→33.759 Å
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Refine LS restraints |
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LS refinement shell |
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