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Yorodumi- PDB-5ogz: Crystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ogz | ||||||
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Title | Crystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A | ||||||
Components | Beta-glucosidase A | ||||||
Keywords | SUGAR BINDING PROTEIN / beta/alpha 8 TIM barrel fold cellobiose binding | ||||||
Function / homology | Function and homology information scopolin beta-glucosidase activity / beta-glucosidase activity / beta-glucosidase / cellulose catabolic process Similarity search - Function | ||||||
Biological species | Ruminiclostridium thermocellum ATCC 27405 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Salama-Alber, O. / Bayer, E. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Ruminiclostridium Thermocellum beta-Glucosidase A Authors: Salama-Alber, O. / Bayer, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ogz.cif.gz | 201.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ogz.ent.gz | 160.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ogz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/5ogz ftp://data.pdbj.org/pub/pdb/validation_reports/og/5ogz | HTTPS FTP |
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-Related structure data
Related structure data | 1qoxS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52602.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ruminiclostridium thermocellum ATCC 27405 (bacteria) Gene: bglA, Cthe_0212 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P26208, beta-glucosidase #2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Water | ChemComp-HOH / | |
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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: 2.28 Å3/Da / Density % sol: 46.01 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Lithium sulfate monohydrate, BIS-TRIS, Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.973 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→93.01 Å / Num. obs: 120756 / % possible obs: 94.61 % / Redundancy: 5 % / Net I/σ(I): 20.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1QOX Resolution: 1.6→93.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.765 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.626 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→93.01 Å
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Refine LS restraints |
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