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- PDB-7pjj: Structure of the Family-3 Glycosyl Hydrolase BcpE2 from Streptomy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pjj | ||||||
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Title | Structure of the Family-3 Glycosyl Hydrolase BcpE2 from Streptomyces scabies | ||||||
![]() | Beta-glucosidase | ||||||
![]() | HYDROLASE / Versatile Beta-glucosidase / O-heteroside hydrolase / Genetic compensation | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase activity / carbohydrate metabolic process Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jadot, C. / Herman, R. / Deflandre, B. / Rigali, S. / Kerff, F. | ||||||
Funding support | 1items
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![]() | ![]() Title: Structure and Function of BcpE2, the Most Promiscuous GH3-Family Glucose Scavenging Beta-Glucosidase. Authors: Deflandre, B. / Jadot, C. / Planckaert, S. / Thiebaut, N. / Stulanovic, N. / Herman, R. / Devreese, B. / Kerff, F. / Rigali, S. #1: ![]() Title: Structure and function of BcpE2, the most promiscuous GH3-family beta-glucosidase for scavenging glucose from heterosides Authors: Deflandre, B. / Jadot, C. / Planckaert, S. / Thiebaut, N. / Stulanovic, N. / Herman, R. / Devreese, B. / Kerff, F. / Rigali, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.9 KB | Display | ![]() |
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PDB format | ![]() | 229.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.5 KB | Display | ![]() |
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Full document | ![]() | 451.1 KB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 37.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4i3gS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 88316.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 87.22 / Gene: SCAB_64101 / Plasmid: pET22b / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 61.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: methylpentane-2,4-dio (MDP) 45%, 0.1M TrisHCl pH 8.5, 0.2M ammonium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9801 Å / Relative weight: 1 |
Reflection | Resolution: 3.086→47.5 Å / Num. obs: 21414 / % possible obs: 99.3 % / Redundancy: 6.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.273 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3.086→3.27 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.22 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3286 / CC1/2: 0.301 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I3G Resolution: 3.086→47.41 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.875 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.428
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Displacement parameters | Biso mean: 90.91 Å2
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Refine analyze | Luzzati coordinate error obs: 0.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.086→47.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.09→3.11 Å
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