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- PDB-8j5l: Structure of GH1 Br2 beta-glucosidase E163Q mutant from bovine ru... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j5l | ||||||
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Title | Structure of GH1 Br2 beta-glucosidase E163Q mutant 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 | ![]() | 383.1 KB | Display | ![]() |
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PDB format | ![]() | 301.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.3 KB | Display | ![]() |
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Full document | ![]() | 500.4 KB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 87.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8j3mC ![]() 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1
NCS ensembles :
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Components
#1: Protein | Mass: 53087.758 Da / Num. of mol.: 4 / Mutation: E163Q 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: 2.58 Å3/Da / Density % sol: 51.62 % |
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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: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.095→50 Å / Num. obs: 115105 / % possible obs: 90.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 46.445 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.109 / Rsym value: 0.097 / Net I/σ(I): 10.25 |
Reflection shell | Resolution: 2.095→2.22 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.55 / Num. unique obs: 19661 / CC1/2: 0.625 / Rrim(I) all: 1.008 / Rsym value: 0.898 / % possible all: 96.4 |
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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: 48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.095→48.139 Å
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Refine LS restraints |
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