+Open data
-Basic information
Entry | Database: PDB / ID: 8xrv | ||||||
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Title | The crystal structure of a GH3 enzyme CcBgl3B with glucose | ||||||
Components | GH3 enzyme CcBgl3B | ||||||
Keywords | HYDROLASE / GH3 enzyme CcBgl3B / glucose | ||||||
Function / homology | beta-D-glucopyranose Function and homology information | ||||||
Biological species | Cellulosimicrobium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 | 8xrv.cif.gz | 864.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8xrv.ent.gz | 711.4 KB | Display | PDB format |
PDBx/mmJSON format | 8xrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/8xrv ftp://data.pdbj.org/pub/pdb/validation_reports/xr/8xrv | HTTPS FTP |
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-Related structure data
Related structure data | 8xrtC 8xruC 8xrxC 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
#1: Protein | Mass: 81757.086 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cellulosimicrobium (bacteria) / Production host: Escherichia coli (E. coli) #2: Sugar | ChemComp-BGC / #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.86 Å3/Da / Density % sol: 68.12 % |
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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: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97775 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.97 Å / Num. obs: 288030 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.4→2.44 Å / Rmerge(I) obs: 0.684 / Num. unique obs: 14283 |
-Processing
Software | Name: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.97 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.15 / 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: 2.4→19.97 Å
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Refine LS restraints |
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LS refinement shell |
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