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- PDB-5xxl: Crystal structure of GH3 beta-glucosidase from Bacteroides thetai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xxl | ||||||
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Title | Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron | ||||||
![]() | Periplasmic beta-glucosidase | ||||||
![]() | HYDROLASE / glycoside hydrolase family 3 / beta-glucosidase | ||||||
Function / homology | ![]() glucan catabolic process / beta-glucosidase / beta-glucosidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nakajima, M. / Ishiguro, R. / Tanaka, N. / Abe, K. / Maeda, T. / Miyanaga, A. / Takahash, Y. / Sugimoto, N. / Nakai, H. / Taguchi, H. | ||||||
![]() | ![]() Title: Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase. Authors: Ishiguro, R. / Tanaka, N. / Abe, K. / Nakajima, M. / Maeda, T. / Miyanaga, A. / Takahashi, Y. / Sugimoto, N. / Nakai, H. / Taguchi, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.3 KB | Display | ![]() |
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PDB format | ![]() | 257.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.1 KB | Display | ![]() |
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Full document | ![]() | 475.2 KB | Display | |
Data in XML | ![]() | 61.7 KB | Display | |
Data in CIF | ![]() | 93.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xxmC ![]() 5xxnC ![]() 5xxoC ![]() 3u4aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 84018.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A predicted signal peptide (residues 2-20) is removed when cloning. Source: (gene. exp.) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3567 / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-PG4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→29.94 Å / Num. obs: 202194 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.6→1.69 Å |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3U4A Resolution: 1.6→29.94 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.085 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.984 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→29.94 Å
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Refine LS restraints |
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