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Yorodumi- PDB-8j5m: Structure of GH1 Br2 beta-glucosidase E350G mutant from bovine ru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j5m | ||||||
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Title | Structure of GH1 Br2 beta-glucosidase E350G mutant from bovine rumen metagenome | ||||||
Components | Beta-glucosidase | ||||||
Keywords | HYDROLASE / Glycoside hydrolase / GH1 / metagenome / beta-glucosidase | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | uncultured bacterium (environmental samples) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.621 Å | ||||||
Authors | Kaenying, W. / Kongsaeree, P.T. / Tagami, T. | ||||||
Funding support | Thailand, 1items
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Citation | Journal: Heliyon / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j5m.cif.gz | 429.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j5m.ent.gz | 335.2 KB | Display | PDB format |
PDBx/mmJSON format | 8j5m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j5/8j5m ftp://data.pdbj.org/pub/pdb/validation_reports/j5/8j5m | HTTPS FTP |
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-Related structure data
Related structure data | 8j3mC 8j5lC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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: 53016.680 Da / Num. of mol.: 4 / Mutation: E350G Source method: isolated from a genetically manipulated source Details: bovine rumen metagenome Source: (gene. exp.) uncultured bacterium (environmental samples) Gene: BG / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1S5SJM8 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.58 Å3/Da / Density % sol: 51.77 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.975 Å |
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: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 271392 / % possible obs: 99.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.082 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.074 / Rsym value: 0.066 / Net I/σ(I): 13.18 |
Reflection shell | Resolution: 1.62→1.72 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.96 / Num. unique obs: 42595 / CC1/2: 0.745 / Rrim(I) all: 0.816 / Rsym value: 0.727 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.621→42.237 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.795 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.076 / ESU R Free: 0.076 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: 23.012 Å2
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Refinement step | Cycle: LAST / Resolution: 1.621→42.237 Å
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Refine LS restraints |
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