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- PDB-5k6o: Structure of a GH3 b-glucosidase from cow rumen metagenome in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5k6o | ||||||
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Title | Structure of a GH3 b-glucosidase from cow rumen metagenome in complex with galactose | ||||||
![]() | B-GLUCOSIDASE | ||||||
![]() | HYDROLASE / GLYCOSIDE HYDROLASE / METAGENOME / B-GLICOSIDASE / FUNCTIONAL FOOD / PREBIOTICS / MICROBIOTA / GALACTOSE | ||||||
Function / homology | beta-D-galactopyranose![]() | ||||||
Biological species | metagenome (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ramirez-Escudero, M. / Sanz-Aparicio, J. | ||||||
![]() | ![]() Title: Structural and Functional Characterization of a Ruminal beta-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology. Authors: Ramirez-Escudero, M. / Del Pozo, M.V. / Marin-Navarro, J. / Gonzalez, B. / Golyshin, P.N. / Polaina, J. / Ferrer, M. / Sanz-Aparicio, 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 | ![]() | 170.3 KB | Display | ![]() |
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PDB format | ![]() | 131.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.7 KB | Display | ![]() |
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Full document | ![]() | 465.4 KB | Display | |
Data in XML | ![]() | 28.3 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k6lSC ![]() 5k6mC ![]() 5k6nC 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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Unit cell |
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Components
#1: Protein | Mass: 101951.930 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: cow rumen / Source: (gene. exp.) metagenome (others) / Gene: glyA1 / Production host: ![]() ![]() | ||||
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#2: Sugar | ChemComp-GAL / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.9 % / Description: Diamond-shaped crystal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 2M (NH4)2SO4, 0.1M Bis-Tris pH 5.5, then soaked in 100mM galactose. PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1271 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→95.08 Å / Num. obs: 44188 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 3.3 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5K6L Resolution: 2.29→95.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.988 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.206 / 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: 47.334 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→95.07 Å
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Refine LS restraints |
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