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Yorodumi- PDB-6lgc: Bombyx mori GH13 sucrose hydrolase complexed with 1-deoxynojirimycin -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lgc | ||||||
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Title | Bombyx mori GH13 sucrose hydrolase complexed with 1-deoxynojirimycin | ||||||
Components | Sucrose hydrolase | ||||||
Keywords | HYDROLASE / Sucrose / Glycoside hydrolase / GH13 / Inhibitor | ||||||
Function / homology | Function and homology information alpha-glucosidase / hydrolase activity, acting on glycosyl bonds / hydrolase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | Bombyx mori (domestic silkworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Miyazaki, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Structure-function analysis of silkworm sucrose hydrolase uncovers the mechanism of substrate specificity in GH13 subfamily 17exo-alpha-glucosidases. Authors: Miyazaki, T. / Park, E.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lgc.cif.gz | 266.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lgc.ent.gz | 208.7 KB | Display | PDB format |
PDBx/mmJSON format | 6lgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/6lgc ftp://data.pdbj.org/pub/pdb/validation_reports/lg/6lgc | HTTPS FTP |
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-Related structure data
Related structure data | 6lgaC 6lgbC 6lgdC 6lgeC 6lgfC 6lggC 6lghC 6lgiC 5brqS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 68739.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bombyx mori (domestic silkworm) / Gene: BmSuh / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A077JI83, UniProt: H9J974*PLUS |
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-Non-polymers , 5 types, 883 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 8% PEG 3350, 0.2 M magnesium acetate, 2 mM 1-deoxynojirimycin |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Jun 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 117900 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.933 / Mean I/σ(I) obs: 3 / Num. unique obs: 17039 / CC1/2: 0.85 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BRQ Resolution: 1.9→48.97 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.867 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.115 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 122.33 Å2 / Biso mean: 29.512 Å2 / Biso min: 16.07 Å2
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Refinement step | Cycle: final / Resolution: 1.9→48.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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