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- PDB-8j3m: Structure of GH1 Br2 beta-glucosidase from bovine rumen metagenome -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j3m | ||||||
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Title | Structure of GH1 Br2 beta-glucosidase from bovine rumen metagenome | ||||||
![]() | Beta-glucosidase | ||||||
![]() | HYDROLASE / Glycoside hydrolase / GH1 / metagenome / beta-glucosidase | ||||||
Function / homology | ![]() scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / cellulose catabolic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kaenying, W. / Kongsaeree, P.T. / Tagami, T. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and mutational analysis of glycoside hydrolase family 1 Br2 beta-glucosidase derived from bovine rumen metagenome. Authors: Kaenying, W. / Tagami, T. / Suwan, E. / Pitsanuwong, C. / Chomngam, S. / Okuyama, M. / Kongsaeree, P. / Kimura, A. / Kongsaeree, P.T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 370.7 KB | Display | ![]() |
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PDB format | ![]() | 294.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8j5lC ![]() 8j5mC C: citing same article ( |
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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: 53088.742 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: bovine rumen metagenome Source: (gene. exp.) ![]() Gene: BG / Plasmid: pET15b / Production host: ![]() ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 0.1M sodium acetate trihydrate pH 7.4, 1.6M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.999→48.26 Å / Num. obs: 135781 / % possible obs: 91.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 45.447 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.083 / Rsym value: 0.073 / Net I/σ(I): 12.03 |
Reflection shell | Resolution: 1.999→2.12 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.76 / Num. unique obs: 23046 / CC1/2: 0.645 / Rrim(I) all: 0.821 / Rsym value: 0.725 / % possible all: 97.1 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.999→48.26 Å
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Refine LS restraints |
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LS refinement shell |
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