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Open data
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Basic information
Entry | Database: PDB / ID: 5jp0 | ||||||||||||
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Title | Bacteroides ovatus Xyloglucan PUL GH3B with bound glucose | ||||||||||||
![]() | Beta-glucosidase BoGH3B | ||||||||||||
![]() | HYDROLASE / Glycoside hydrolase / GH3 | ||||||||||||
Function / homology | ![]() symbiotic process benefiting host / xyloglucan catabolic process / scopolin beta-glucosidase activity / beta-glucosidase / beta-glucosidase activity / periplasmic space Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Hemsworth, G.R. / Thompson, A.J. / Stepper, J. / Sobala, L.F. / Coyle, T. / Larsbrink, J. / Spadiut, O. / Stubbs, K.A. / Brumer, H. / Davies, G.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut. Authors: Hemsworth, G.R. / Thompson, A.J. / Stepper, J. / Sobala, F. / Coyle, T. / Larsbrink, J. / Spadiut, O. / Goddard-Borger, E.D. / Stubbs, K.A. / Brumer, H. / Davies, G.J. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 584 KB | Display | ![]() |
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PDB format | ![]() | 478.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.5 KB | Display | ![]() |
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Full document | ![]() | 456.1 KB | Display | |
Data in XML | ![]() | 53.4 KB | Display | |
Data in CIF | ![]() | 76.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5jouC ![]() 5jovC ![]() 5jowC ![]() 5joxC ![]() 5joyC ![]() 5jozC ![]() 1ex1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: _ / Auth seq-ID: 26 - 782 / Label seq-ID: 4 - 760
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Components
#1: Protein | Mass: 86483.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium acetate, 15-25% PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→47.57 Å / Num. obs: 72918 / % possible obs: 99.9 % / Redundancy: 8.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.923 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ex1 Resolution: 2.3→47.57 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 13.096 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.311 / ESU R Free: 0.205 / 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: 35.059 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→47.57 Å
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Refine LS restraints |
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