+Open data
-Basic information
Entry | Database: PDB / ID: 6m6l | ||||||
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Title | The crystal structure of glycosidase hydrolyzing Notoginsenoside | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / Glycosidase / Notoginsenoside | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Kribbella flavida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Wang, R.F. | ||||||
Citation | Journal: To Be Published Title: Characterization and Structural Elucidation of Enhanced Catalytic Activity upon Engineering Glycosidase KfGH01 for the Production of Vina-ginsenoside R7 Authors: Wang, R.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m6l.cif.gz | 213 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m6l.ent.gz | 167.1 KB | Display | PDB format |
PDBx/mmJSON format | 6m6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6m6l_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6m6l_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6m6l_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 6m6l_validation.cif.gz | 69.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/6m6l ftp://data.pdbj.org/pub/pdb/validation_reports/m6/6m6l | HTTPS FTP |
-Related structure data
Related structure data | 6m6mC 3ta9S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49331.020 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) (bacteria) Strain: DSM 17836 / JCM 10339 / NBRC 14399 / Gene: Kfla_5268 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: D2PL27, beta-glucosidase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Sugar | ChemComp-XYP / | #5: Water | ChemComp-HOH / | 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: 2.38 Å3/Da / Density % sol: 48.28 % Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M Sodium citrate tribasic dehydrate (pH 5.6), 0.2 M ammonium acetate and PEG 4000 (30%, w/v) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 147102 / % possible obs: 96.9 % / Redundancy: 3.8 % / CC1/2: 1 / Net I/σ(I): 29.5 |
Reflection shell | Resolution: 1.49→1.5 Å / Num. unique obs: 147102 / CC1/2: 1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TA9 Resolution: 1.5→35.371 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.93 Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→35.371 Å
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Refine LS restraints |
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LS refinement shell |
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