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Yorodumi- PDB-8xrx: The crystal structure of a GH3 enzyme CcBgl3B with glucose and ge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8xrx | ||||||
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Title | The crystal structure of a GH3 enzyme CcBgl3B with glucose and gentiobiose | ||||||
Components | GH3 enzyme CcBgl3B | ||||||
Keywords | HYDROLASE / GH3 enzyme CcBgl3B / glucose / gentiobiose | ||||||
Function / homology | beta-D-glucopyranose / alpha-D-glucopyranose Function and homology information | ||||||
Biological species | Cellulosimicrobium cellulans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Su, J.Y. | ||||||
Funding support | China, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 beta-glucosidase: An X-ray crystallographic and biochemical study. Authors: Hu, C. / Wang, Y. / Wang, W. / Cui, W. / Jia, X. / Mayo, K.H. / Zhou, Y. / Su, J. / Yuan, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8xrx.cif.gz | 795.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xrx.ent.gz | 655.6 KB | Display | PDB format |
PDBx/mmJSON format | 8xrx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/8xrx ftp://data.pdbj.org/pub/pdb/validation_reports/xr/8xrx | HTTPS FTP |
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-Related structure data
Related structure data | 8xrtC 8xruC 8xrvC 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 81757.086 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulosimicrobium cellulans (bacteria) Production host: Escherichia coli (E. coli) |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | #4: Sugar | #5: Sugar | ChemComp-GLC / | |
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-Non-polymers , 2 types, 409 molecules
#3: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
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: 4.02 Å3/Da / Density % sol: 69.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97538 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97538 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→19.95 Å / Num. obs: 264973 / % possible obs: 99 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.538 / Num. unique obs: 11550 |
-Processing
Software | Name: PHENIX / Version: (1.10.1_2155: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→19.948 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→19.948 Å
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Refine LS restraints |
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LS refinement shell |
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