+Open data
-Basic information
Entry | Database: PDB / ID: 6lga | ||||||
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Title | Bombyx mori GH13 sucrose hydrolase | ||||||
Components | Sucrose hydrolase | ||||||
Keywords | HYDROLASE / Sucrose / Glycoside hydrolase / GH13 | ||||||
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: 1.85 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 | 6lga.cif.gz | 275.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lga.ent.gz | 215.1 KB | Display | PDB format |
PDBx/mmJSON format | 6lga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lg/6lga ftp://data.pdbj.org/pub/pdb/validation_reports/lg/6lga | HTTPS FTP |
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-Related structure data
Related structure data | 6lgbC 6lgcC 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) / Strain (production host): BL21(DE3) / References: UniProt: A0A077JI83, UniProt: H9J974*PLUS |
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-Non-polymers , 5 types, 1234 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PGE / | #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: 2.82 Å3/Da / Density % sol: 56.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 3350, 0.2 M magnesium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 16, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 127062 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 12546 / CC1/2: 0.786 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5BRQ Resolution: 1.85→48.91 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.435 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.104 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: 104.51 Å2 / Biso mean: 22.431 Å2 / Biso min: 11.69 Å2
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Refinement step | Cycle: final / Resolution: 1.85→48.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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